From b189eade7d74c80d9c3cce6c5eb7a74f201f927a Mon Sep 17 00:00:00 2001 From: Jingru923 <47444880+Jingru923@users.noreply.github.com> Date: Fri, 12 Jan 2024 12:49:13 +0100 Subject: [PATCH 01/82] No more warning in Ribasim Python when plotting model without edges (#940) Fixes #937 --- python/ribasim/ribasim/geometry/edge.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/python/ribasim/ribasim/geometry/edge.py b/python/ribasim/ribasim/geometry/edge.py index c3a509186..7148e9ee1 100644 --- a/python/ribasim/ribasim/geometry/edge.py +++ b/python/ribasim/ribasim/geometry/edge.py @@ -74,7 +74,8 @@ def plot(self, **kwargs) -> Axes: where_flow = self.get_where_edge_type("flow") where_control = self.get_where_edge_type("control") - self.df[where_flow].plot(**kwargs_flow) + if not self.df[where_flow].empty: + self.df[where_flow].plot(**kwargs_flow) if where_control.any(): self.df[where_control].plot(**kwargs_control) From 13707d3ffe92cbce3b36039ce80c626067e0fd88 Mon Sep 17 00:00:00 2001 From: Martijn Visser Date: Fri, 12 Jan 2024 16:24:47 +0100 Subject: [PATCH 02/82] Update our depdendencies (#942) Since we just released, now is a good moment to update our dependencies in our pixi and Julia environments. This fixes one issue noted by @deltamarnix, now our versions of pandas and pandas-stubs are the same: ```yaml name: pandas version: 2.1.4 name: pandas-stubs version: 2.1.4.231227 ``` This also extends our root julia environment a bit, adding https://github.com/JuliaDebug/Infiltrator.jl which is useful for debugging, and adding dependencies of the core project, such that we can use them directly in the root environment. --- Manifest.toml | 395 +- Project.toml | 9 + core/src/config.jl | 2 +- core/test/docs.toml | 2 +- docs/core/usage.qmd | 1 - docs/schema/Solver.schema.json | 14 +- docs/schema/Toml.schema.json | 2 +- pixi.lock | 6475 ++++++++++++++++++++------------ 8 files changed, 4212 insertions(+), 2688 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index 3f635a725..a4e91fb27 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -2,12 +2,12 @@ julia_version = "1.10.0" manifest_format = "2.0" -project_hash = "d7ee772a6ce028def5673f584203e74ddba25b58" +project_hash = "a2e54351da64b7dac3109810459579d647b75bb7" [[deps.ADTypes]] -git-tree-sha1 = "332e5d7baeff8497b923b730b994fa480601efc7" +git-tree-sha1 = "41c37aa88889c171f1300ceac1313c06e891d245" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "0.2.5" +version = "0.2.6" [[deps.ANSIColoredPrinters]] git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c" @@ -21,9 +21,9 @@ version = "0.4.4" [[deps.Accessors]] deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Test"] -git-tree-sha1 = "a7055b939deae2455aa8a67491e034f735dd08d3" +git-tree-sha1 = "cb96992f1bec110ad211b7e410e57ddf7944c16f" uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" -version = "0.1.33" +version = "0.1.35" [deps.Accessors.extensions] AccessorsAxisKeysExt = "AxisKeys" @@ -40,9 +40,9 @@ version = "0.1.33" [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] -git-tree-sha1 = "02f731463748db57cc2ebfbd9fbc9ce8280d3433" +git-tree-sha1 = "cde29ddf7e5726c9fb511f340244ea3481267608" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.7.1" +version = "3.7.2" weakdeps = ["StaticArrays"] [deps.Adapt.extensions] @@ -65,9 +65,9 @@ version = "0.2.0" [[deps.ArrayInterface]] deps = ["Adapt", "LinearAlgebra", "Requires", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "247efbccf92448be332d154d6ca56b9fcdd93c31" +git-tree-sha1 = "bbec08a37f8722786d87bedf84eae19c020c4efa" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.6.1" +version = "7.7.0" [deps.ArrayInterface.extensions] ArrayInterfaceBandedMatricesExt = "BandedMatrices" @@ -85,17 +85,27 @@ version = "7.6.1" StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" +[[deps.ArrayLayouts]] +deps = ["FillArrays", "LinearAlgebra"] +git-tree-sha1 = "a45ec4acc9d905f94b47243cff666820bb107789" +uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" +version = "1.5.2" +weakdeps = ["SparseArrays"] + + [deps.ArrayLayouts.extensions] + ArrayLayoutsSparseArraysExt = "SparseArrays" + [[deps.Arrow]] deps = ["ArrowTypes", "BitIntegers", "CodecLz4", "CodecZstd", "ConcurrentUtilities", "DataAPI", "Dates", "EnumX", "LoggingExtras", "Mmap", "PooledArrays", "SentinelArrays", "Tables", "TimeZones", "TranscodingStreams", "UUIDs"] -git-tree-sha1 = "954666e252835c4cf8819ce4ffaf31073c1b7233" +git-tree-sha1 = "cd893c29839c524ca2c5944b8e05f26e299df105" uuid = "69666777-d1a9-59fb-9406-91d4454c9d45" -version = "2.6.2" +version = "2.7.0" [[deps.ArrowTypes]] deps = ["Sockets", "UUIDs"] -git-tree-sha1 = "8c37bfdf1b689c6677bbfc8986968fe641f6a299" +git-tree-sha1 = "404265cd8128a2515a81d5eae16de90fdef05101" uuid = "31f734f8-188a-4ce0-8406-c8a06bd891cd" -version = "2.2.2" +version = "2.3.0" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -110,9 +120,9 @@ version = "0.1.0" [[deps.BenchmarkTools]] deps = ["JSON", "Logging", "Printf", "Profile", "Statistics", "UUIDs"] -git-tree-sha1 = "d9a9701b899b30332bbcb3e1679c41cce81fb0e8" +git-tree-sha1 = "f1f03a9fa24271160ed7e73051fba3c1a759b53f" uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" -version = "1.3.2" +version = "1.4.0" [[deps.BitIntegers]] deps = ["Random"] @@ -132,11 +142,6 @@ git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" version = "1.0.8+0" -[[deps.CEnum]] -git-tree-sha1 = "eb4cb44a499229b3b8426dcfb5dd85333951ff90" -uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" -version = "0.4.2" - [[deps.CPUSummary]] deps = ["CpuId", "IfElse", "PrecompileTools", "Static"] git-tree-sha1 = "601f7e7b3d36f18790e2caf83a882d88e9b71ff1" @@ -145,9 +150,9 @@ version = "0.2.4" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra"] -git-tree-sha1 = "e0af648f0692ec1691b5d094b8724ba1346281cf" +git-tree-sha1 = "c1deebd76f7a443d527fc0430d5758b8b2112ed8" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.18.0" +version = "1.19.1" weakdeps = ["SparseArrays"] [deps.ChainRulesCore.extensions] @@ -184,10 +189,10 @@ uuid = "944b1d66-785c-5afd-91f1-9de20f533193" version = "0.7.3" [[deps.CodecZstd]] -deps = ["CEnum", "TranscodingStreams", "Zstd_jll"] -git-tree-sha1 = "849470b337d0fa8449c21061de922386f32949d9" +deps = ["TranscodingStreams", "Zstd_jll"] +git-tree-sha1 = "f69e46bf7b307d15a896b57d5b3321c01cd64923" uuid = "6b39b394-51ab-5f42-8807-6242bab2b4c2" -version = "0.7.2" +version = "0.8.1" [[deps.CommonSolve]] git-tree-sha1 = "0eee5eb66b1cf62cd6ad1b460238e60e4b09400c" @@ -201,10 +206,10 @@ uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" version = "0.3.0" [[deps.Compat]] -deps = ["UUIDs"] -git-tree-sha1 = "8a62af3e248a8c4bad6b32cbbe663ae02275e32c" +deps = ["TOML", "UUIDs"] +git-tree-sha1 = "ed2ebb1ff7550226ddb584ba8352facf8d9ffb22" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.10.0" +version = "4.11.0" weakdeps = ["Dates", "LinearAlgebra"] [deps.Compat.extensions] @@ -217,9 +222,9 @@ version = "1.0.5+1" [[deps.ComponentArrays]] deps = ["ArrayInterface", "ChainRulesCore", "ForwardDiff", "Functors", "LinearAlgebra", "PackageExtensionCompat", "StaticArrayInterface", "StaticArraysCore"] -git-tree-sha1 = "d30eb4d89c791a64e698546c1e0e0e488cd99da5" +git-tree-sha1 = "0bcacba787140924e954304216dcc09f968176ca" uuid = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66" -version = "0.15.5" +version = "0.15.7" [deps.ComponentArrays.extensions] ComponentArraysAdaptExt = "Adapt" @@ -315,28 +320,29 @@ uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" version = "1.6.1" [[deps.DataInterpolations]] -deps = ["LinearAlgebra", "PrettyTables", "RecipesBase", "RecursiveArrayTools", "Reexport", "Requires"] -git-tree-sha1 = "97b5c6115165fc9f99908cbdd2ea4c0efda0843e" +deps = ["LinearAlgebra", "PrettyTables", "RecipesBase", "Reexport", "Requires"] +git-tree-sha1 = "99f979d5e9b67c2aeee701c3683037ac8d75bdd6" uuid = "82cc6244-b520-54b8-b5a6-8a565e85f1d0" -version = "4.5.0" +version = "4.6.0" [deps.DataInterpolations.extensions] DataInterpolationsChainRulesCoreExt = "ChainRulesCore" - DataInterpolationsOptimExt = "Optim" + DataInterpolationsOptimExt = ["ForwardDiff", "Optim"] DataInterpolationsRegularizationToolsExt = "RegularizationTools" DataInterpolationsSymbolicsExt = "Symbolics" [deps.DataInterpolations.weakdeps] ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" Optim = "429524aa-4258-5aef-a3af-852621145aeb" RegularizationTools = "29dad682-9a27-4bc3-9c72-016788665182" Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "3dbd312d370723b6bb43ba9d02fc36abade4518d" +git-tree-sha1 = "ac67408d9ddf207de5cfa9a97e114352430f01ed" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.15" +version = "0.18.16" [[deps.DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -347,12 +353,6 @@ version = "1.0.0" deps = ["Printf"] uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" -[[deps.DelimitedFiles]] -deps = ["Mmap"] -git-tree-sha1 = "9e2f36d3c96a820c678f2f1f1782582fcf685bae" -uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" -version = "1.9.1" - [[deps.Dictionaries]] deps = ["Indexing", "Random", "Serialization"] git-tree-sha1 = "e82c3c97b5b4ec111f3c1b55228cebc7510525a2" @@ -361,9 +361,9 @@ version = "0.3.25" [[deps.DiffEqBase]] deps = ["ArrayInterface", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces"] -git-tree-sha1 = "309efb205c30d43b595466283bbecf2769283e22" +git-tree-sha1 = "044648af911974c3928058c1f8c83f159dece274" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.141.0" +version = "6.145.6" [deps.DiffEqBase.extensions] DiffEqBaseChainRulesCoreExt = "ChainRulesCore" @@ -391,9 +391,9 @@ version = "6.141.0" [[deps.DiffEqCallbacks]] deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "Functors", "LinearAlgebra", "Markdown", "NLsolve", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "4e4de57a0ac47b2f20aae62f132355b058e9f0cd" +git-tree-sha1 = "cf334da651a6e42c50e1477d6ab978f1b8be3057" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" -version = "2.34.0" +version = "2.36.1" [deps.DiffEqCallbacks.weakdeps] OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" @@ -418,9 +418,9 @@ version = "0.1.6" [[deps.Distances]] deps = ["LinearAlgebra", "Statistics", "StatsAPI"] -git-tree-sha1 = "5225c965635d8c21168e32a12954675e7bea1151" +git-tree-sha1 = "66c4c81f259586e8f002eacebc177e1fb06363b0" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.10" +version = "0.10.11" weakdeps = ["ChainRulesCore", "SparseArrays"] [deps.Distances.extensions] @@ -460,10 +460,13 @@ uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" version = "1.0.4" [[deps.EnzymeCore]] -deps = ["Adapt"] -git-tree-sha1 = "2efe862de93cd87f620ad6ac9c9e3f83f1b2841b" +git-tree-sha1 = "59c44d8fbc651c0395d8a6eda64b05ce316f58b4" uuid = "f151be2c-9106-41f4-ab19-57ee4f262869" -version = "0.6.4" +version = "0.6.5" +weakdeps = ["Adapt"] + + [deps.EnzymeCore.extensions] + AdaptExt = "Adapt" [[deps.ExponentialUtilities]] deps = ["Adapt", "ArrayInterface", "GPUArraysCore", "GenericSchur", "LinearAlgebra", "PrecompileTools", "Printf", "SparseArrays", "libblastrampoline_jll"] @@ -500,18 +503,18 @@ version = "2.0.0" [[deps.FileIO]] deps = ["Pkg", "Requires", "UUIDs"] -git-tree-sha1 = "299dc33549f68299137e51e6d49a13b5b1da9673" +git-tree-sha1 = "c5c28c245101bd59154f649e19b038d15901b5dc" uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" -version = "1.16.1" +version = "1.16.2" [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] deps = ["LinearAlgebra", "Random"] -git-tree-sha1 = "28e4e9c4b7b162398ec8004bdabe9a90c78c122d" +git-tree-sha1 = "5b93957f6dcd33fc343044af3d48c215be2562f1" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.8.0" +version = "1.9.3" [deps.FillArrays.extensions] FillArraysPDMatsExt = "PDMats" @@ -525,9 +528,9 @@ version = "1.8.0" [[deps.FiniteDiff]] deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays"] -git-tree-sha1 = "c6e4a1fbe73b31a3dea94b1da449503b8830c306" +git-tree-sha1 = "73d1214fec245096717847c62d389a5d2ac86504" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.21.1" +version = "2.22.0" [deps.FiniteDiff.extensions] FiniteDiffBandedMatricesExt = "BandedMatrices" @@ -633,6 +636,12 @@ git-tree-sha1 = "ce1566720fd6b19ff3411404d4b977acd4814f9f" uuid = "313cdc1a-70c2-5d6a-ae34-0150d3930a38" version = "1.1.1" +[[deps.Infiltrator]] +deps = ["InteractiveUtils", "Markdown", "REPL", "UUIDs"] +git-tree-sha1 = "04de041e4590428cccbb026d86e5d670513be2e3" +uuid = "5903a43b-9cc3-4c30-8d17-598619ec4e9b" +version = "1.6.4" + [[deps.Inflate]] git-tree-sha1 = "ea8031dea4aff6bd41f1df8f2fdfb25b33626381" uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" @@ -644,16 +653,11 @@ git-tree-sha1 = "9cc2baf75c6d09f9da536ddf58eb2f29dedaf461" uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48" version = "1.4.0" -[[deps.IntegerMathUtils]] -git-tree-sha1 = "b8ffb903da9f7b8cf695a8bead8e01814aa24b30" -uuid = "18e54dd8-cb9d-406c-a71d-865a43cbb235" -version = "0.1.2" - [[deps.IntelOpenMP_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "ad37c091f7d7daf900963171600d7c1c5c3ede32" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "5fdf2fe6724d8caabf43b557b84ce53f3b7e2f6b" uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0" -version = "2023.2.0+0" +version = "2024.0.2+0" [[deps.InteractiveUtils]] deps = ["Markdown"] @@ -676,9 +680,9 @@ uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" version = "0.2.2" [[deps.IterTools]] -git-tree-sha1 = "4ced6667f9974fc5c5943fa5e2ef1ca43ea9e450" +git-tree-sha1 = "42d5f897009e7ff2cf88db414a389e5ed1bdd023" uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e" -version = "1.8.0" +version = "1.10.0" [[deps.IteratorInterfaceExtensions]] git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" @@ -687,9 +691,9 @@ version = "1.0.0" [[deps.JLD2]] deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "PrecompileTools", "Printf", "Reexport", "Requires", "TranscodingStreams", "UUIDs"] -git-tree-sha1 = "9bbb5130d3b4fa52846546bca4791ecbdfb52730" +git-tree-sha1 = "853b9e0b876e8c7093a824c4f83c619d23525e64" uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819" -version = "0.4.38" +version = "0.4.43" [[deps.JLLWrappers]] deps = ["Artifacts", "Preferences"] @@ -705,15 +709,19 @@ version = "0.21.4" [[deps.JSON3]] deps = ["Dates", "Mmap", "Parsers", "PrecompileTools", "StructTypes", "UUIDs"] -git-tree-sha1 = "95220473901735a0f4df9d1ca5b171b568b2daa3" +git-tree-sha1 = "eb3edce0ed4fa32f75a0a11217433c31d56bd48b" uuid = "0f8b85d8-7281-11e9-16c2-39a750bddbf1" -version = "1.13.2" +version = "1.14.0" +weakdeps = ["ArrowTypes"] + + [deps.JSON3.extensions] + JSON3ArrowExt = ["ArrowTypes"] [[deps.JuMP]] -deps = ["LinearAlgebra", "MacroTools", "MathOptInterface", "MutableArithmetics", "OrderedCollections", "Printf", "SnoopPrecompile", "SparseArrays"] -git-tree-sha1 = "25b2fcda4d455b6f93ac753730d741340ba4a4fe" +deps = ["LinearAlgebra", "MacroTools", "MathOptInterface", "MutableArithmetics", "OrderedCollections", "PrecompileTools", "Printf", "SparseArrays"] +git-tree-sha1 = "adef1dfbafeab635664fb3249b58be8d290ed49d" uuid = "4076af6c-e467-56ae-b986-b466b2749572" -version = "1.16.0" +version = "1.18.1" [deps.JuMP.extensions] JuMPDimensionalDataExt = "DimensionalData" @@ -723,9 +731,9 @@ version = "1.16.0" [[deps.JuliaInterpreter]] deps = ["CodeTracking", "InteractiveUtils", "Random", "UUIDs"] -git-tree-sha1 = "e49bce680c109bc86e3e75ebcb15040d6ad9e1d3" +git-tree-sha1 = "04663b9e1eb0d0eabf76a6d0752e0dac83d53b36" uuid = "aa1ae85d-cabe-5617-a682-6adf51b2e16a" -version = "0.9.27" +version = "0.9.28" [[deps.KLU]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"] @@ -735,21 +743,15 @@ version = "0.4.1" [[deps.Krylov]] deps = ["LinearAlgebra", "Printf", "SparseArrays"] -git-tree-sha1 = "17e462054b42dcdda73e9a9ba0c67754170c88ae" +git-tree-sha1 = "8a6837ec02fe5fb3def1abc907bb802ef11a0729" uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7" -version = "0.9.4" +version = "0.9.5" [[deps.LaTeXStrings]] git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" version = "1.3.1" -[[deps.LatticeRules]] -deps = ["Random"] -git-tree-sha1 = "7f5b02258a3ca0221a6a9710b0a0a2e8fb4957fe" -uuid = "73f95e8e-ec14-4e6a-8b18-0d2e271c4e55" -version = "0.0.1" - [[deps.LayoutPointers]] deps = ["ArrayInterface", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface"] git-tree-sha1 = "62edfee3211981241b57ff1cedf4d74d79519277" @@ -762,6 +764,16 @@ git-tree-sha1 = "1370f8202dac30758f3c345f9909b97f53d87d3f" uuid = "50d2b5c4-7a5e-59d5-8109-a42b560f39c0" version = "0.15.1" +[[deps.LazyArrays]] +deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "MatrixFactorizations", "SparseArrays"] +git-tree-sha1 = "9cfca23ab83b0dfac93cb1a1ef3331ab9fe596a5" +uuid = "5078a376-72f3-5289-bfd5-ec5146d43c02" +version = "1.8.3" +weakdeps = ["StaticArrays"] + + [deps.LazyArrays.extensions] + LazyArraysStaticArraysExt = "StaticArrays" + [[deps.LazyArtifacts]] deps = ["Artifacts", "Pkg"] uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" @@ -773,10 +785,10 @@ uuid = "1d6d02ad-be62-4b6b-8a6d-2f90e265016e" version = "0.2.0" [[deps.Legolas]] -deps = ["Arrow", "ConstructionBase", "Tables", "UUIDs"] -git-tree-sha1 = "e7a7f5005f05f60006c8bdb4f0c3bedaf9fd5e4f" +deps = ["Arrow", "ArrowTypes", "ConstructionBase", "Tables", "UUIDs"] +git-tree-sha1 = "b38a5941d383981ddef92f48b7cd016f249632fa" uuid = "741b9549-f6ed-4911-9fbf-4a1c0c97f0cd" -version = "0.5.15" +version = "0.5.18" [[deps.LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] @@ -816,16 +828,16 @@ deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LinearSolve]] -deps = ["ArrayInterface", "ConcreteStructs", "DocStringExtensions", "EnumX", "EnzymeCore", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "Libdl", "LinearAlgebra", "MKL_jll", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "UnPack"] -git-tree-sha1 = "051943b8b8e81c548e9d099d6eb3d3ed23093c35" +deps = ["ArrayInterface", "ConcreteStructs", "DocStringExtensions", "EnumX", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "Libdl", "LinearAlgebra", "MKL_jll", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "StaticArraysCore", "UnPack"] +git-tree-sha1 = "6f8e084deabe3189416c4e505b1c53e1b590cae8" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "2.20.0" +version = "2.22.1" [deps.LinearSolve.extensions] LinearSolveBandedMatricesExt = "BandedMatrices" LinearSolveBlockDiagonalsExt = "BlockDiagonals" LinearSolveCUDAExt = "CUDA" - LinearSolveEnzymeExt = "Enzyme" + LinearSolveEnzymeExt = ["Enzyme", "EnzymeCore"] LinearSolveFastAlmostBandedMatricesExt = ["FastAlmostBandedMatrices"] LinearSolveHYPREExt = "HYPRE" LinearSolveIterativeSolversExt = "IterativeSolvers" @@ -840,6 +852,7 @@ version = "2.20.0" BlockDiagonals = "0a1fb500-61f7-11e9-3c65-f5ef3456f9f0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" FastAlmostBandedMatrices = "9d29842c-ecb8-4973-b1e9-a27b1157504e" HYPRE = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771" IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153" @@ -887,9 +900,9 @@ weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] [[deps.LoweredCodeUtils]] deps = ["JuliaInterpreter"] -git-tree-sha1 = "0b8cf121228f7dae022700c1c11ac1f04122f384" +git-tree-sha1 = "38756922d32476c8f41f73560b910fc805a5a103" uuid = "6f1432cf-f94c-5a45-995e-cdbf5db27b0b" -version = "2.3.2" +version = "2.4.3" [[deps.Lz4_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -898,16 +911,16 @@ uuid = "5ced341a-0733-55b8-9ab6-a4889d929147" version = "1.9.4+0" [[deps.MKL_jll]] -deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"] -git-tree-sha1 = "eb006abbd7041c28e0d16260e50a24f8f9104913" +deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl"] +git-tree-sha1 = "72dc3cf284559eb8f53aa593fe62cb33f83ed0c0" uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" -version = "2023.2.0+0" +version = "2024.0.0+0" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" +git-tree-sha1 = "b211c553c199c111d998ecdaf7623d1b89b69f93" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.11" +version = "0.5.12" [[deps.ManualMemory]] git-tree-sha1 = "bcaef4fc7a0cfe2cba636d84cda54b5e4e4ca3cd" @@ -926,9 +939,21 @@ version = "1.1.0" [[deps.MathOptInterface]] deps = ["BenchmarkTools", "CodecBzip2", "CodecZlib", "DataStructures", "ForwardDiff", "JSON", "LinearAlgebra", "MutableArithmetics", "NaNMath", "OrderedCollections", "PrecompileTools", "Printf", "SparseArrays", "SpecialFunctions", "Test", "Unicode"] -git-tree-sha1 = "70ea2892b8bfffecc0387ba1a6a21192814f120c" +git-tree-sha1 = "e2ae8cf5ac6daf5a3959f7f6ded9c2028b61d09d" uuid = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" -version = "1.22.0" +version = "1.25.1" + +[[deps.MatrixFactorizations]] +deps = ["ArrayLayouts", "LinearAlgebra", "Printf", "Random"] +git-tree-sha1 = "78f6e33434939b0ac9ba1df81e6d005ee85a7396" +uuid = "a3b82374-2e81-5b9e-98ce-41277c0e4c87" +version = "2.1.0" + +[[deps.MaybeInplace]] +deps = ["ArrayInterface", "LinearAlgebra", "MacroTools", "SparseArrays"] +git-tree-sha1 = "a85c6a98c9e5a2a7046bc1bb89f28a3241e1de4d" +uuid = "bb5d69b7-63fc-4a16-80bd-7e42200c7bdb" +version = "0.1.1" [[deps.MbedTLS]] deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "NetworkOptions", "Random", "Sockets"] @@ -943,9 +968,9 @@ version = "2.28.2+1" [[deps.MetaGraphsNext]] deps = ["Graphs", "JLD2", "SimpleTraits"] -git-tree-sha1 = "8dd4f3f8a643d53e61ff9115749f522c35a38f3f" +git-tree-sha1 = "a385fe5aa1384647e55c0c8773457b71e9b08518" uuid = "fa8bd995-216d-47f1-8a91-f3b68fbeb377" -version = "0.6.0" +version = "0.7.0" [[deps.Missings]] deps = ["DataAPI"] @@ -973,9 +998,9 @@ version = "0.2.4" [[deps.MutableArithmetics]] deps = ["LinearAlgebra", "SparseArrays", "Test"] -git-tree-sha1 = "6985021d02ab8c509c841bb8b2becd3145a7b490" +git-tree-sha1 = "806eea990fb41f9b36f1253e5697aa645bf6a9f8" uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" -version = "1.3.3" +version = "1.4.0" [[deps.NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] @@ -1000,26 +1025,43 @@ uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" version = "1.2.0" [[deps.NonlinearSolve]] -deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "EnumX", "FastBroadcast", "FiniteDiff", "ForwardDiff", "LineSearches", "LinearAlgebra", "LinearSolve", "PrecompileTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "6166ccd8f79c93c636ca61ab4cd18f555932563d" +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "EnumX", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "LazyArrays", "LineSearches", "LinearAlgebra", "LinearSolve", "MaybeInplace", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] +git-tree-sha1 = "72b036b728461272ae1b1c3f7096cb4c319d8793" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "2.8.2" +version = "3.4.0" [deps.NonlinearSolve.extensions] NonlinearSolveBandedMatricesExt = "BandedMatrices" NonlinearSolveFastLevenbergMarquardtExt = "FastLevenbergMarquardt" + NonlinearSolveFixedPointAccelerationExt = "FixedPointAcceleration" NonlinearSolveLeastSquaresOptimExt = "LeastSquaresOptim" + NonlinearSolveMINPACKExt = "MINPACK" + NonlinearSolveNLsolveExt = "NLsolve" + NonlinearSolveSIAMFANLEquationsExt = "SIAMFANLEquations" + NonlinearSolveSpeedMappingExt = "SpeedMapping" + NonlinearSolveSymbolicsExt = "Symbolics" + NonlinearSolveZygoteExt = "Zygote" [deps.NonlinearSolve.weakdeps] BandedMatrices = "aae01518-5342-5314-be14-df237901396f" FastLevenbergMarquardt = "7a0df574-e128-4d35-8cbd-3d84502bf7ce" + FixedPointAcceleration = "817d07cb-a79a-5c30-9a31-890123675176" LeastSquaresOptim = "0fc2ff8b-aaa3-5acd-a817-1944a5e08891" + MINPACK = "4854310b-de5a-5eb6-a2a5-c1dee2bd17f9" + NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56" + SIAMFANLEquations = "084e46ad-d928-497d-ad5e-07fa361a48c4" + SpeedMapping = "f1835b91-879b-4a3f-a438-e4baacf14412" + Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.OffsetArrays]] -deps = ["Adapt"] -git-tree-sha1 = "2ac17d29c523ce1cd38e27785a7d23024853a4bb" +git-tree-sha1 = "6a731f2b5c03157418a20c12195eb4b74c8f8621" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.12.10" +version = "1.13.0" +weakdeps = ["Adapt"] + + [deps.OffsetArrays.extensions] + OffsetArraysAdaptExt = "Adapt" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] @@ -1043,16 +1085,16 @@ uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" version = "1.6.3" [[deps.OrdinaryDiffEq]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLNLSolve", "SciMLOperators", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "5f9e7ce227d0e447c3803cc05ef5d8f75f84b9ea" +deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FillArrays", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "MacroTools", "MuladdMacro", "NonlinearSolve", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] +git-tree-sha1 = "7c6738f21fba2ccd07b7eaa9d23b437a8a97f1a1" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "6.59.3" +version = "6.69.0" [[deps.PackageCompiler]] deps = ["Artifacts", "Glob", "LazyArtifacts", "Libdl", "Pkg", "Printf", "RelocatableFolders", "TOML", "UUIDs", "p7zip_jll"] -git-tree-sha1 = "8b880733c61c4a99a069302390de2d057ee166ce" +git-tree-sha1 = "48d4429862157ad5500c4f61444db1b8c32e0a2b" uuid = "9b87118b-4619-50d2-8e1e-99f35a4d4d9d" -version = "2.1.16" +version = "2.1.17" [[deps.PackageExtensionCompat]] git-tree-sha1 = "fb28e33b8a95c4cee25ce296c817d89cc2e53518" @@ -1068,9 +1110,9 @@ version = "0.12.3" [[deps.Parsers]] deps = ["Dates", "PrecompileTools", "UUIDs"] -git-tree-sha1 = "a935806434c9d4c506ba941871b327b96d41f2bf" +git-tree-sha1 = "8489905bcdbcfac64d1daa51ca07c0d8f0283821" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.8.0" +version = "2.8.1" [[deps.Pkg]] deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] @@ -1096,10 +1138,10 @@ uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720" version = "1.4.3" [[deps.PreallocationTools]] -deps = ["Adapt", "ArrayInterface", "ForwardDiff", "Requires"] -git-tree-sha1 = "f739b1b3cc7b9949af3b35089931f2b58c289163" +deps = ["Adapt", "ArrayInterface", "ForwardDiff"] +git-tree-sha1 = "64bb68f76f789f5fe5930a80af310f19cdafeaed" uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" -version = "0.4.12" +version = "0.4.17" [deps.PreallocationTools.extensions] PreallocationToolsReverseDiffExt = "ReverseDiff" @@ -1125,12 +1167,6 @@ git-tree-sha1 = "88b895d13d53b5577fd53379d913b9ab9ac82660" uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" version = "2.3.1" -[[deps.Primes]] -deps = ["IntegerMathUtils"] -git-tree-sha1 = "1d05623b5952aed1307bf8b43bec8b8d1ef94b6e" -uuid = "27ebfcd6-29c5-5fa9-bf4b-fb8fc14df3ae" -version = "0.5.5" - [[deps.Printf]] deps = ["Unicode"] uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" @@ -1145,18 +1181,6 @@ git-tree-sha1 = "80d919dee55b9c50e8d9e2da5eeafff3fe58b539" uuid = "33c8b6b6-d38a-422a-b730-caa89a2f386c" version = "0.1.4" -[[deps.QuasiMonteCarlo]] -deps = ["Accessors", "ConcreteStructs", "LatticeRules", "LinearAlgebra", "Primes", "Random", "Requires", "Sobol", "StatsBase"] -git-tree-sha1 = "cc086f8485bce77b6187141e1413c3b55f9a4341" -uuid = "8a4e6c94-4038-4cdc-81c3-7e6ffdb2a71b" -version = "0.3.3" - - [deps.QuasiMonteCarlo.extensions] - QuasiMonteCarloDistributionsExt = "Distributions" - - [deps.QuasiMonteCarlo.weakdeps] - Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" - [[deps.REPL]] deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" @@ -1167,9 +1191,9 @@ uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" [[deps.ReTestItems]] deps = ["Dates", "Logging", "LoggingExtras", "Pkg", "Serialization", "Sockets", "Test", "TestEnv"] -git-tree-sha1 = "e8dd0646b221f3b75af2f36f83f509e2dde8dbe8" +git-tree-sha1 = "68a7d4fd86f12c2fc6dec60d566f033a10ffb5fb" uuid = "817f1d60-ba6b-4fd5-9520-3cf149f6a823" -version = "1.22.0" +version = "1.23.0" [[deps.RecipesBase]] deps = ["PrecompileTools"] @@ -1178,18 +1202,20 @@ uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" version = "1.3.4" [[deps.RecursiveArrayTools]] -deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "d7087c013e8a496ff396bae843b1e16d9a30ede8" +deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "SparseArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] +git-tree-sha1 = "4943624c0e437ddf6362a82e5319bc8e83d80857" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.38.10" +version = "3.5.2" [deps.RecursiveArrayTools.extensions] + RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" RecursiveArrayToolsMeasurementsExt = "Measurements" RecursiveArrayToolsMonteCarloMeasurementsExt = "MonteCarloMeasurements" RecursiveArrayToolsTrackerExt = "Tracker" RecursiveArrayToolsZygoteExt = "Zygote" [deps.RecursiveArrayTools.weakdeps] + FastBroadcast = "7034ab61-46d4-4ed7-9d0f-46aef9175898" Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" @@ -1220,15 +1246,15 @@ version = "1.3.0" [[deps.Revise]] deps = ["CodeTracking", "Distributed", "FileWatching", "JuliaInterpreter", "LibGit2", "LoweredCodeUtils", "OrderedCollections", "Pkg", "REPL", "Requires", "UUIDs", "Unicode"] -git-tree-sha1 = "6990168abf3fe9a6e34ebb0e05aaaddf6572189e" +git-tree-sha1 = "3fe4e5b9cdbb9bbc851c57b149e516acc07f8f72" uuid = "295af30f-e4ad-537b-8983-00126c2a3abe" -version = "3.5.10" +version = "3.5.13" [[deps.Ribasim]] deps = ["Accessors", "Arrow", "BasicModelInterface", "CodecLz4", "CodecZstd", "ComponentArrays", "Configurations", "DBInterface", "DataInterpolations", "DataStructures", "Dates", "Dictionaries", "DiffEqCallbacks", "EnumX", "FiniteDiff", "ForwardDiff", "Graphs", "HiGHS", "IterTools", "JuMP", "Legolas", "Logging", "LoggingExtras", "MetaGraphsNext", "OrdinaryDiffEq", "PreallocationTools", "SQLite", "SciMLBase", "SparseArrays", "StructArrays", "Tables", "TerminalLoggers", "TimeZones", "TimerOutputs", "TranscodingStreams"] path = "core" uuid = "aac5e3d9-0b8f-4d4f-8241-b1a7a9632635" -version = "0.5.1" +version = "0.6.0" [[deps.RuntimeGeneratedFunctions]] deps = ["ExprTools", "SHA", "Serialization"] @@ -1264,10 +1290,10 @@ uuid = "76ed43ae-9a5d-5a62-8c75-30186b810ce8" version = "3.43.0+0" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FillArrays", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "QuasiMonteCarlo", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "d432b4c4cc922fb7b21b555c138aa87f9fb7beb8" +deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FillArrays", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] +git-tree-sha1 = "b2714ddd879525c825f427e861f5059a96b287f7" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.9.1" +version = "2.18.0" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -1286,12 +1312,6 @@ version = "2.9.1" RCall = "6f49c342-dc21-5d91-9882-a32aef131414" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" -[[deps.SciMLNLSolve]] -deps = ["DiffEqBase", "LineSearches", "NLsolve", "Reexport", "SciMLBase"] -git-tree-sha1 = "765b788339abd7d983618c09cfc0192e2b6b15fd" -uuid = "e9a6253c-8580-4d32-9898-8661bb511710" -version = "0.1.9" - [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] git-tree-sha1 = "51ae235ff058a64815e0a2c34b1db7578a06813d" @@ -1324,16 +1344,16 @@ deps = ["Distributed", "Mmap", "Random", "Serialization"] uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383" [[deps.SimpleNonlinearSolve]] -deps = ["ArrayInterface", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "PrecompileTools", "Reexport", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "69b1a53374dd14d7c165d98cb646aeb5f36f8d07" +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "MaybeInplace", "PrecompileTools", "Reexport", "SciMLBase", "StaticArraysCore"] +git-tree-sha1 = "8d672bd91dc432fb286b6d4bcf1a5dc417e932a3" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "0.1.25" +version = "1.2.0" [deps.SimpleNonlinearSolve.extensions] - SimpleNonlinearSolveNNlibExt = "NNlib" + SimpleNonlinearSolvePolyesterForwardDiffExt = "PolyesterForwardDiff" [deps.SimpleNonlinearSolve.weakdeps] - NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" + PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b" [[deps.SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] @@ -1346,18 +1366,6 @@ git-tree-sha1 = "58e6353e72cde29b90a69527e56df1b5c3d8c437" uuid = "ce78b400-467f-4804-87d8-8f486da07d0a" version = "1.1.0" -[[deps.SnoopPrecompile]] -deps = ["Preferences"] -git-tree-sha1 = "e760a70afdcd461cf01a575947738d359234665c" -uuid = "66db9d55-30c0-4569-8b51-7e840670fc0c" -version = "1.0.3" - -[[deps.Sobol]] -deps = ["DelimitedFiles", "Random"] -git-tree-sha1 = "5a74ac22a9daef23705f010f72c81d6925b19df8" -uuid = "ed01d8cd-4d21-5b2a-85b4-cc3bdc58bad4" -version = "1.5.0" - [[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" @@ -1369,9 +1377,9 @@ version = "1.1.0" [[deps.SortingAlgorithms]] deps = ["DataStructures"] -git-tree-sha1 = "5165dfb9fd131cf0c6957a3a7605dede376e7b63" +git-tree-sha1 = "66e0a8e672a0bdfca2c3f5937efb8538b9ddc085" uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" -version = "1.2.0" +version = "1.2.1" [[deps.SparseArrays]] deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] @@ -1380,9 +1388,9 @@ version = "1.10.0" [[deps.SparseDiffTools]] deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "Tricks", "UnPack", "VertexSafeGraphs"] -git-tree-sha1 = "07272c80c278947baca092df0a01da4a10622ad5" +git-tree-sha1 = "c281e11db4eacb36a292a054bac83c5a0aca2a26" uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" -version = "2.13.0" +version = "2.15.0" [deps.SparseDiffTools.extensions] SparseDiffToolsEnzymeExt = "Enzyme" @@ -1418,9 +1426,9 @@ version = "0.8.8" [[deps.StaticArrayInterface]] deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Requires", "SparseArrays", "Static", "SuiteSparse"] -git-tree-sha1 = "03fec6800a986d191f64f5c0996b59ed526eda25" +git-tree-sha1 = "5d66818a39bb04bf328e92bc933ec5b4ee88e436" uuid = "0d7ed370-da01-4f52-bd93-41d350b8b718" -version = "1.4.1" +version = "1.5.0" weakdeps = ["OffsetArrays", "StaticArrays"] [deps.StaticArrayInterface.extensions] @@ -1429,12 +1437,13 @@ weakdeps = ["OffsetArrays", "StaticArrays"] [[deps.StaticArrays]] deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] -git-tree-sha1 = "5ef59aea6f18c25168842bded46b16662141ab87" +git-tree-sha1 = "4e17a790909b17f7bf1496e3aec138cf01b60b3b" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.7.0" -weakdeps = ["Statistics"] +version = "1.9.0" +weakdeps = ["ChainRulesCore", "Statistics"] [deps.StaticArrays.extensions] + StaticArraysChainRulesCoreExt = "ChainRulesCore" StaticArraysStatisticsExt = "Statistics" [[deps.StaticArraysCore]] @@ -1453,12 +1462,6 @@ git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" version = "1.7.0" -[[deps.StatsBase]] -deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "1d77abd07f617c4868c33d4f5b9e1dbb2643c9cf" -uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.34.2" - [[deps.StrideArraysCore]] deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] git-tree-sha1 = "d6415f66f3d89c615929af907fdc6a3e17af0d8c" @@ -1493,10 +1496,9 @@ uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" version = "7.2.1+1" [[deps.SymbolicIndexingInterface]] -deps = ["DocStringExtensions"] -git-tree-sha1 = "f8ab052bfcbdb9b48fad2c80c873aa0d0344dfe5" +git-tree-sha1 = "74502f408d99fc217a9d7cd901d9ffe45af892b1" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" -version = "0.2.2" +version = "0.3.3" [[deps.TOML]] deps = ["Dates"] @@ -1567,10 +1569,13 @@ uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" version = "0.5.23" [[deps.TranscodingStreams]] -deps = ["Random", "Test"] -git-tree-sha1 = "9a6ae7ed916312b41236fcef7e0af564ef934769" +git-tree-sha1 = "1fbeaaca45801b4ba17c251dd8603ef24801dd84" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.9.13" +version = "0.10.2" +weakdeps = ["Random", "Test"] + + [deps.TranscodingStreams.extensions] + TestExt = ["Test", "Random"] [[deps.TriangularSolve]] deps = ["CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "LoopVectorization", "Polyester", "Static", "VectorizationBase"] @@ -1603,9 +1608,9 @@ uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" [[deps.VectorizationBase]] deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static", "StaticArrayInterface"] -git-tree-sha1 = "b182207d4af54ac64cbc71797765068fdeff475d" +git-tree-sha1 = "7209df901e6ed7489fe9b7aa3e46fb788e15db85" uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" -version = "0.21.64" +version = "0.21.65" [[deps.VersionParsing]] git-tree-sha1 = "58d6e80b4ee071f5efd07fda82cb9fbe17200868" diff --git a/Project.toml b/Project.toml index 36cc6a120..6df86f2b1 100644 --- a/Project.toml +++ b/Project.toml @@ -3,9 +3,18 @@ authors = ["Deltares and contributors "] description = "Meta-project used to share the Manifest of Ribasim and its dependents" [deps] +Arrow = "69666777-d1a9-59fb-9406-91d4454c9d45" +BasicModelInterface = "59605e27-edc0-445a-b93d-c09a3a50b330" +Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6" +Infiltrator = "5903a43b-9cc3-4c30-8d17-598619ec4e9b" +MetaGraphsNext = "fa8bd995-216d-47f1-8a91-f3b68fbeb377" +OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" ReTestItems = "817f1d60-ba6b-4fd5-9520-3cf149f6a823" Revise = "295af30f-e4ad-537b-8983-00126c2a3abe" Ribasim = "aac5e3d9-0b8f-4d4f-8241-b1a7a9632635" +SQLite = "0aa819cd-b072-5ff4-a722-6bc24af294d9" +SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462" +Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" TestEnv = "1e6cf692-eddd-4d53-88a5-2d735e33781b" TimeZones = "f269a46b-ccf7-5d73-abea-4c690281aa53" create_binaries = "3cfb6a46-05f0-43df-bb16-bf763deb14b4" diff --git a/core/src/config.jl b/core/src/config.jl index 3cd3e28ea..bd785473d 100644 --- a/core/src/config.jl +++ b/core/src/config.jl @@ -80,7 +80,7 @@ const nodetypes = collect(keys(nodekinds)) saveat::Union{Float64, Vector{Float64}} = Float64[] adaptive::Bool = true dt::Union{Float64, Nothing} = nothing - dtmin::Union{Float64, Nothing} = nothing + dtmin::Float64 = 0.0 dtmax::Union{Float64, Nothing} = nothing force_dtmin::Bool = false abstol::Float64 = 1e-6 diff --git a/core/test/docs.toml b/core/test/docs.toml index cbc1a1e46..f2c0b136b 100644 --- a/core/test/docs.toml +++ b/core/test/docs.toml @@ -23,7 +23,7 @@ algorithm = "QNDF" # optional, default "QNDF" saveat = [] # optional, default [], which saves every timestep adaptive = true # optional, default true dt = 0.0 # optional when adaptive = true, default automatically determined -dtmin = 0.0 # optional, default automatically determined +dtmin = 0.0 # optional, default 0.0 dtmax = 0.0 # optional, default length of simulation force_dtmin = false # optional, default false abstol = 1e-6 # optional, default 1e-6 diff --git a/docs/core/usage.qmd b/docs/core/usage.qmd index 6cf12c20e..1a2915196 100644 --- a/docs/core/usage.qmd +++ b/docs/core/usage.qmd @@ -43,7 +43,6 @@ When `adaptive = true`, `dt` only applies to the initial stepsize, and by defaul When `adaptive = false` a suitable `dt` must always be provided. The value is in seconds, so `dt = 3600.0` corresponds to an hourly timestep. When `adaptive = true`, `dtmin` and `dtmax` control the minimum and maximum allowed `dt`. -By default these depend on the problem and algorithm. If a smaller `dt` than `dtmin` is needed to meet the set error tolerances, the simulation stops, unless `force_dtmin` is set to `true`. `force_dtmin` is off by default to ensure an accurate solution. diff --git a/docs/schema/Solver.schema.json b/docs/schema/Solver.schema.json index 5d5be176a..4b3f6c236 100644 --- a/docs/schema/Solver.schema.json +++ b/docs/schema/Solver.schema.json @@ -44,16 +44,9 @@ "default": null }, "dtmin": { - "format": "default", - "anyOf": [ - { - "type": "null" - }, - { - "type": "number" - } - ], - "default": null + "format": "double", + "type": "number", + "default": 0 }, "dtmax": { "format": "default", @@ -102,6 +95,7 @@ "algorithm", "saveat", "adaptive", + "dtmin", "force_dtmin", "abstol", "reltol", diff --git a/docs/schema/Toml.schema.json b/docs/schema/Toml.schema.json index 43c92d215..1fce57eba 100644 --- a/docs/schema/Toml.schema.json +++ b/docs/schema/Toml.schema.json @@ -42,7 +42,7 @@ ], "adaptive": true, "dt": null, - "dtmin": null, + "dtmin": 0, "dtmax": null, "force_dtmin": false, "abstol": 1.0e-6, diff --git a/pixi.lock b/pixi.lock index 6124341f1..0e765a511 100644 --- a/pixi.lock +++ b/pixi.lock @@ -98,6 +98,8 @@ package: noarch: python size: 17026 timestamp: 1696634393637 + purls: + - pkg:pypi/annotated-types - platform: osx-64 name: annotated-types version: 0.6.0 @@ -119,6 +121,8 @@ package: noarch: python size: 17026 timestamp: 1696634393637 + purls: + - pkg:pypi/annotated-types - platform: osx-arm64 name: annotated-types version: 0.6.0 @@ -140,6 +144,8 @@ package: noarch: python size: 17026 timestamp: 1696634393637 + purls: + - pkg:pypi/annotated-types - platform: win-64 name: annotated-types version: 0.6.0 @@ -161,9 +167,11 @@ package: noarch: python size: 17026 timestamp: 1696634393637 + purls: + - pkg:pypi/annotated-types - platform: linux-64 name: anyio - version: 4.1.0 + version: 4.2.0 category: main manager: conda dependencies: @@ -171,10 +179,11 @@ package: - idna >=2.8 - python >=3.8 - sniffio >=1.1 - url: https://conda.anaconda.org/conda-forge/noarch/anyio-4.1.0-pyhd8ed1ab_0.conda + - typing_extensions >=4.1 + url: https://conda.anaconda.org/conda-forge/noarch/anyio-4.2.0-pyhd8ed1ab_0.conda hash: - md5: 76a3b574717769c4c937c2afa2f1069f - sha256: d9d64b29d8a4f58a8d5f9cb0af80b70fd4e038a6e328b039899f7cd93863a82e + md5: 81ce9f3d9697b534d95118bb86c8a07e + sha256: 68458e31bdf3334f0e85f08767718ca9bc35bc2a79a6c503942ac99da98e510a build: pyhd8ed1ab_0 arch: x86_64 subdir: linux-64 @@ -185,11 +194,13 @@ package: license: MIT license_family: MIT noarch: python - size: 100177 - timestamp: 1700835583246 + size: 101592 + timestamp: 1702909362897 + purls: + - pkg:pypi/anyio - platform: osx-64 name: anyio - version: 4.1.0 + version: 4.2.0 category: main manager: conda dependencies: @@ -197,10 +208,11 @@ package: - idna >=2.8 - python >=3.8 - sniffio >=1.1 - url: https://conda.anaconda.org/conda-forge/noarch/anyio-4.1.0-pyhd8ed1ab_0.conda + - typing_extensions >=4.1 + url: https://conda.anaconda.org/conda-forge/noarch/anyio-4.2.0-pyhd8ed1ab_0.conda hash: - md5: 76a3b574717769c4c937c2afa2f1069f - sha256: d9d64b29d8a4f58a8d5f9cb0af80b70fd4e038a6e328b039899f7cd93863a82e + md5: 81ce9f3d9697b534d95118bb86c8a07e + sha256: 68458e31bdf3334f0e85f08767718ca9bc35bc2a79a6c503942ac99da98e510a build: pyhd8ed1ab_0 arch: x86_64 subdir: osx-64 @@ -211,11 +223,13 @@ package: license: MIT license_family: MIT noarch: python - size: 100177 - timestamp: 1700835583246 + size: 101592 + timestamp: 1702909362897 + purls: + - pkg:pypi/anyio - platform: osx-arm64 name: anyio - version: 4.1.0 + version: 4.2.0 category: main manager: conda dependencies: @@ -223,10 +237,11 @@ package: - idna >=2.8 - python >=3.8 - sniffio >=1.1 - url: https://conda.anaconda.org/conda-forge/noarch/anyio-4.1.0-pyhd8ed1ab_0.conda + - typing_extensions >=4.1 + url: https://conda.anaconda.org/conda-forge/noarch/anyio-4.2.0-pyhd8ed1ab_0.conda hash: - md5: 76a3b574717769c4c937c2afa2f1069f - sha256: d9d64b29d8a4f58a8d5f9cb0af80b70fd4e038a6e328b039899f7cd93863a82e + md5: 81ce9f3d9697b534d95118bb86c8a07e + sha256: 68458e31bdf3334f0e85f08767718ca9bc35bc2a79a6c503942ac99da98e510a build: pyhd8ed1ab_0 arch: aarch64 subdir: osx-arm64 @@ -237,11 +252,13 @@ package: license: MIT license_family: MIT noarch: python - size: 100177 - timestamp: 1700835583246 + size: 101592 + timestamp: 1702909362897 + purls: + - pkg:pypi/anyio - platform: win-64 name: anyio - version: 4.1.0 + version: 4.2.0 category: main manager: conda dependencies: @@ -249,10 +266,11 @@ package: - idna >=2.8 - python >=3.8 - sniffio >=1.1 - url: https://conda.anaconda.org/conda-forge/noarch/anyio-4.1.0-pyhd8ed1ab_0.conda + - typing_extensions >=4.1 + url: https://conda.anaconda.org/conda-forge/noarch/anyio-4.2.0-pyhd8ed1ab_0.conda hash: - md5: 76a3b574717769c4c937c2afa2f1069f - sha256: d9d64b29d8a4f58a8d5f9cb0af80b70fd4e038a6e328b039899f7cd93863a82e + md5: 81ce9f3d9697b534d95118bb86c8a07e + sha256: 68458e31bdf3334f0e85f08767718ca9bc35bc2a79a6c503942ac99da98e510a build: pyhd8ed1ab_0 arch: x86_64 subdir: win-64 @@ -263,8 +281,10 @@ package: license: MIT license_family: MIT noarch: python - size: 100177 - timestamp: 1700835583246 + size: 101592 + timestamp: 1702909362897 + purls: + - pkg:pypi/anyio - platform: osx-64 name: appnope version: 0.1.3 @@ -285,6 +305,8 @@ package: noarch: python size: 8095 timestamp: 1649077760928 + purls: + - pkg:pypi/appnope - platform: osx-arm64 name: appnope version: 0.1.3 @@ -305,17 +327,19 @@ package: noarch: python size: 8095 timestamp: 1649077760928 + purls: + - pkg:pypi/appnope - platform: linux-64 name: argcomplete - 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ucrt >=10.0.20348.0 - vc >=14.2,<15 - vc14_runtime >=14.29.30139 - url: https://conda.anaconda.org/conda-forge/win-64/xerces-c-3.2.4-h63175ca_3.conda + url: https://conda.anaconda.org/conda-forge/win-64/xerces-c-3.2.5-h63175ca_0.conda hash: - md5: 28c6b90f40c9c37d3334ba8225143690 - sha256: 76e5ba07c06947ff7dcee6e9fe47e436e7a5ec5d94ad23102186769459af1403 - build: h63175ca_3 + md5: b1e07902b6bb7833db8cc4ec32f32dc7 + sha256: 21328b0442f2f86ad5bf14481ed60f56a8ebb765a68d158a57ec6f32eb55762b + build: h63175ca_0 arch: x86_64 subdir: win-64 - build_number: 3 + build_number: 0 license: Apache-2.0 license_family: Apache - size: 3509286 - timestamp: 1692976908514 + size: 3574165 + timestamp: 1703093650967 - platform: linux-64 name: xkeyboard-config version: '2.40' @@ -37137,6 +38630,8 @@ package: noarch: python size: 18460 timestamp: 1681486998644 + purls: + - pkg:pypi/xmipy - platform: osx-64 name: xmipy version: 1.3.1 @@ -37158,6 +38653,8 @@ package: noarch: python size: 18460 timestamp: 1681486998644 + purls: + - pkg:pypi/xmipy - platform: osx-arm64 name: xmipy version: 1.3.1 @@ -37179,6 +38676,8 @@ package: noarch: python size: 18460 timestamp: 1681486998644 + purls: + - pkg:pypi/xmipy - platform: win-64 name: xmipy version: 1.3.1 @@ -37200,6 +38699,8 @@ package: noarch: python size: 18460 timestamp: 1681486998644 + purls: + - pkg:pypi/xmipy - platform: linux-64 name: xorg-kbproto version: 1.0.7 @@ -37569,6 +39070,8 @@ package: noarch: python size: 36184 timestamp: 1698325478381 + purls: + - pkg:pypi/xyzservices - platform: osx-64 name: xyzservices version: 2023.10.1 @@ -37589,6 +39092,8 @@ package: noarch: python size: 36184 timestamp: 1698325478381 + purls: + - pkg:pypi/xyzservices - platform: osx-arm64 name: xyzservices version: 2023.10.1 @@ -37609,6 +39114,8 @@ package: noarch: python size: 36184 timestamp: 1698325478381 + purls: + - pkg:pypi/xyzservices - platform: win-64 name: xyzservices version: 2023.10.1 @@ -37629,6 +39136,8 @@ package: noarch: python size: 36184 timestamp: 1698325478381 + purls: + - pkg:pypi/xyzservices - platform: linux-64 name: xz version: 5.2.6 @@ -37880,6 +39389,8 @@ package: noarch: python size: 18954 timestamp: 1695255262261 + purls: + - pkg:pypi/zipp - platform: osx-64 name: zipp version: 3.17.0 @@ -37900,6 +39411,8 @@ package: noarch: python size: 18954 timestamp: 1695255262261 + purls: + - pkg:pypi/zipp - platform: osx-arm64 name: zipp version: 3.17.0 @@ -37920,6 +39433,8 @@ package: noarch: python size: 18954 timestamp: 1695255262261 + purls: + - pkg:pypi/zipp - platform: win-64 name: zipp version: 3.17.0 @@ -37940,6 +39455,8 @@ package: noarch: python size: 18954 timestamp: 1695255262261 + purls: + - pkg:pypi/zipp - platform: linux-64 name: zlib version: 1.2.13 From 96737b0a2546aadad4292c3bb198441db3aa4a62 Mon Sep 17 00:00:00 2001 From: Hofer-Julian <30049909+Hofer-Julian@users.noreply.github.com> Date: Mon, 15 Jan 2024 12:58:09 +0100 Subject: [PATCH 03/82] Adapt download links (#949) Fixes #946 --- README.md | 5 ++--- docs/index.qmd | 7 ++----- 2 files changed, 4 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 771a49339..dd5894f1a 100644 --- a/README.md +++ b/README.md @@ -20,15 +20,14 @@ libraries, notably [ModelingToolkit.jl](https://mtk.sciml.ai/stable/). For most users the [latest release](https://github.com/Deltares/Ribasim/releases/latest) is recommended, it can be downloaded here: -- Ribasim executable: [ribasim_cli.zip](https://github.com/Deltares/Ribasim/releases/latest/download/ribasim_cli.zip). -- Python package: [ribasim-0.6.2-py3-none-any.whl](https://github.com/Deltares/Ribasim/releases/latest/download/ribasim-0.6.2-py3-none-any.whl) +- Ribasim executable - Linux: [ribasim_cli_linux.zip](https://github.com/Deltares/Ribasim/releases/latest/download/ribasim_cli_linux.zip) +- Ribasim executable - Windows: [ribasim_cli_windows.zip](https://github.com/Deltares/Ribasim/releases/latest/download/ribasim_cli_windows.zip) - QGIS plugin: [ribasim_qgis.zip](https://github.com/Deltares/Ribasim/releases/latest/download/ribasim_qgis.zip). - Generated testmodels: [generated_testmodels.zip](https://github.com/Deltares/Ribasim/releases/latest/download/generated_testmodels.zip) The nightly builds contain the latest developments and can be found below. It is important to either use the release or nightly for all components. - Ribasim executable: [ribasim_cli.zip](https://ribasim.s3.eu-west-3.amazonaws.com/teamcity/Ribasim_Ribasim/BuildRibasimCliWindows/latest/ribasim_cli.zip). -- Python package: [ribasim-0.6.2-py3-none-any.whl](https://ribasim.s3.eu-west-3.amazonaws.com/teamcity/Ribasim_Ribasim/BuildRibasimCliWindows/latest/ribasim-0.6.2-py3-none-any.whl) - QGIS plugin: [ribasim_qgis.zip](https://ribasim.s3.eu-west-3.amazonaws.com/teamcity/Ribasim_Ribasim/BuildRibasimCliWindows/latest/ribasim_qgis.zip). Currently only Windows builds for `ribasim_cli.zip` are available. diff --git a/docs/index.qmd b/docs/index.qmd index cd20c2c1b..7cb85040d 100644 --- a/docs/index.qmd +++ b/docs/index.qmd @@ -27,17 +27,14 @@ libraries, notably [DifferentialEquations.jl](https://docs.sciml.ai/DiffEqDocs/s # Download {#sec-download} -For most users the [latest release](https://github.com/Deltares/Ribasim/releases/latest) is recommended, it can be downloaded here: - -- Ribasim executable: [ribasim_cli.zip](https://github.com/Deltares/Ribasim/releases/latest/download/ribasim_cli.zip). -- Python package: [ribasim-0.6.2-py3-none-any.whl](https://github.com/Deltares/Ribasim/releases/latest/download/ribasim-0.6.2-py3-none-any.whl) +- Ribasim executable - Linux: [ribasim_cli_linux.zip](https://github.com/Deltares/Ribasim/releases/latest/download/ribasim_cli_linux.zip) +- Ribasim executable - Windows: [ribasim_cli_windows.zip](https://github.com/Deltares/Ribasim/releases/latest/download/ribasim_cli_windows.zip) - QGIS plugin: [ribasim_qgis.zip](https://github.com/Deltares/Ribasim/releases/latest/download/ribasim_qgis.zip). - Generated testmodels: [generated_testmodels.zip](https://github.com/Deltares/Ribasim/releases/latest/download/generated_testmodels.zip) The nightly builds contain the latest developments and can be found below. It is important to either use the release or nightly for all components. - Ribasim executable: [ribasim_cli.zip](https://ribasim.s3.eu-west-3.amazonaws.com/teamcity/Ribasim_Ribasim/BuildRibasimCliWindows/latest/ribasim_cli.zip). -- Python package: [ribasim-0.6.2-py3-none-any.whl](https://ribasim.s3.eu-west-3.amazonaws.com/teamcity/Ribasim_Ribasim/BuildRibasimCliWindows/latest/ribasim-0.6.2-py3-none-any.whl) - QGIS plugin: [ribasim_qgis.zip](https://ribasim.s3.eu-west-3.amazonaws.com/teamcity/Ribasim_Ribasim/BuildRibasimCliWindows/latest/ribasim_qgis.zip). Currently only Windows builds for `ribasim_cli.zip` are available. From eb21b63db60afa4baeb79e3da25397903b7b8895 Mon Sep 17 00:00:00 2001 From: Huite Date: Mon, 15 Jan 2024 14:32:21 +0100 Subject: [PATCH 04/82] Launch debug julia (#953) Add an entry to launch.json to debug Julia --- .vscode/launch.json | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/.vscode/launch.json b/.vscode/launch.json index 7aa67e7b8..ba6cd8152 100644 --- a/.vscode/launch.json +++ b/.vscode/launch.json @@ -1,6 +1,15 @@ { "version": "0.2.0", "configurations": [ + { + "type": "julia", + "request": "launch", + "name": "Julia: current file", + "program": "${file}", + "stopOnEntry": false, + "cwd": "${workspaceFolder}", + "juliaEnv": "${command:activeJuliaEnvironment}" + }, { "name": "Ribasim QGIS: Attach to QGIS", "type": "python", From 197f6f064456e8fe04f51833c944965c7fe87cd0 Mon Sep 17 00:00:00 2001 From: Maarten Pronk <8655030+evetion@users.noreply.github.com> Date: Mon, 15 Jan 2024 15:09:00 +0100 Subject: [PATCH 05/82] [ci] Fix intermittent QGIS test failures. (#939) Long story short, we did a `sleep 10` to wait for the container to be ready. I removed it, and now start a displayserver (`xvfb-run -a`, separate from the container one) as part of the test, which seems to be much more reliable. --- .docker/compose.yml | 1 + .docker/start.sh | 2 -- .docker/test.sh | 2 +- ribasim_qgis/tests/test_load_plugin.py | 3 +++ 4 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.docker/compose.yml b/.docker/compose.yml index 2405ad9c2..aebb15bf7 100644 --- a/.docker/compose.yml +++ b/.docker/compose.yml @@ -9,3 +9,4 @@ services: environment: - CI=true - DISPLAY=:99 + tty: true diff --git a/.docker/start.sh b/.docker/start.sh index 7a3be80e7..b000c6f32 100755 --- a/.docker/start.sh +++ b/.docker/start.sh @@ -4,8 +4,6 @@ set -euxo pipefail source .env docker compose -f compose.yml up -d --force-recreate --remove-orphans -echo "Wait 10 seconds" -sleep 10 echo "Installation of the plugin Ribasim" docker exec -t qgis sh -c "qgis_setup.sh ${PLUGIN_NAME}" echo "Containers are running" diff --git a/.docker/test.sh b/.docker/test.sh index d895510c5..eb432e3d8 100755 --- a/.docker/test.sh +++ b/.docker/test.sh @@ -3,4 +3,4 @@ set -euxo pipefail source .env -docker exec -t qgis sh -c "cd /tests_directory && qgis_testrunner.sh ${PLUGIN_NAME}.tests" +docker exec -t qgis sh -c "cd /tests_directory && xvfb-run -a qgis_testrunner.sh ${PLUGIN_NAME}.tests" diff --git a/ribasim_qgis/tests/test_load_plugin.py b/ribasim_qgis/tests/test_load_plugin.py index 382383ae2..1868379aa 100644 --- a/ribasim_qgis/tests/test_load_plugin.py +++ b/ribasim_qgis/tests/test_load_plugin.py @@ -4,9 +4,12 @@ class TestPlugin(unittest.TestCase): def test_plugin_is_loaded(self): + """Test plugin is properly loaded and appears in QGIS plugins.""" plugin = plugins.get("ribasim_qgis") self.assertTrue(plugin, "Ribasim plugin not loaded") + +class TestDock(unittest.TestCase): def test_load_dock(self): """Triggers Ribasim button and checks that Dock is added""" From d6fb63730a066ae9b352b0922d2ed7e768b02968 Mon Sep 17 00:00:00 2001 From: Huite Date: Mon, 15 Jan 2024 16:01:14 +0100 Subject: [PATCH 06/82] Set initial level after parameter creation (#955) Fixes #952 The basin level would remain at 0.0 otherwise. Then the callback is called at t=0.0, and the resulting interpolated subgrid levels are nonsense. --- core/src/bmi.jl | 3 +++ core/test/run_models_test.jl | 4 +++- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/core/src/bmi.jl b/core/src/bmi.jl index b7b62e200..d2d7f43bb 100644 --- a/core/src/bmi.jl +++ b/core/src/bmi.jl @@ -83,6 +83,9 @@ function BMI.initialize(T::Type{Model}, config::Config)::Model end storages end + # Synchronize level with storage + set_current_basin_properties!(parameters.basin, storage) + @assert length(storage) == n "Basin / state length differs from number of Basins" # Integrals for PID control integral = zeros(length(parameters.pid_control.node_id)) diff --git a/core/test/run_models_test.jl b/core/test/run_models_test.jl index e0b058e0a..995b07032 100644 --- a/core/test/run_models_test.jl +++ b/core/test/run_models_test.jl @@ -77,11 +77,13 @@ @test basin.level[1] ≈ 0.044711584 # The exporter interpolates 1:1 for three subgrid elements, but shifted by 1.0 meter. + basin_level = basin.level[1] @test length(p.subgrid.level) == 3 @test diff(p.subgrid.level) ≈ [-1.0, 2.0] # TODO The original subgrid IDs are lost and mapped to 1, 2, 3 @test subgrid.subgrid_id[1:3] == [11, 22, 33] broken = true - @test subgrid.subgrid_level[1:3] == [0.0, -1.0, 1.0] + @test subgrid.subgrid_level[1:3] ≈ + [basin_level, basin_level - 1.0, basin_level + 1.0] @test subgrid.subgrid_level[(end - 2):end] == p.subgrid.level end end From ebd2f65ae0e35e2e0ae59006cfc93b7d6d295776 Mon Sep 17 00:00:00 2001 From: Hofer-Julian <30049909+Hofer-Julian@users.noreply.github.com> Date: Mon, 15 Jan 2024 16:12:30 +0100 Subject: [PATCH 07/82] Reflect current release process in docs (#948) Fixes #944 --- docs/contribute/release.qmd | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/docs/contribute/release.qmd b/docs/contribute/release.qmd index 570972965..bd298f551 100644 --- a/docs/contribute/release.qmd +++ b/docs/contribute/release.qmd @@ -34,10 +34,21 @@ The nightly download links for the Ribasim Python wheels contain the version num ## Create a new release -Create a [new release](https://github.com/Deltares/Ribasim/releases/new). -Give it a tag like `v2023.08.0`, filling in the current year, month and a sequential "MICRO" number. +Create a new tag like `v2023.08.0`, filling in the current year, month and a sequential "MICRO" number. This follows `vYYYY.0M.MICRO` from [calver](https://calver.org/). -For [v2023.09.0](https://github.com/Deltares/Ribasim/releases/tag/v2023.09.0) I used the "Generate release notes" button, which I then manually edited to copy the most important changes for users to the top in the form of [Keep a Changelog](https://keepachangelog.com/en/1.0.0/). +This can be done by executing: +```bash +git tag +``` +Then push the tags: +```bash +git push --tags +``` + +This will trigger a workflow on TeamCity that will publish a new release on GitHub as soon as it is finished. +You can follow the progress [here](https://dpcbuild.deltares.nl/buildConfiguration/Ribasim_Ribasim_MakeGitHubRelease?mode=builds). +It also auto-generates a changelog. +You'll probably want to curate that by rearranging the most important changes for users to the top in the form of [Keep a Changelog](https://keepachangelog.com/en/1.0.0/). The possibly long list of generated release notes can put below an "All changes" collapsed item as such: ``` From ed802dcab410b970aea59abd324b2a70cc9061c3 Mon Sep 17 00:00:00 2001 From: Martijn Visser Date: Mon, 15 Jan 2024 16:17:53 +0100 Subject: [PATCH 08/82] Fix and change table sorting in Python (#903) Fixes the first two items of #601. Also adds a test. --- docs/core/usage.qmd | 46 ++++++++++++++-------------- python/ribasim/ribasim/config.py | 40 ++++++++++++++++++++---- python/ribasim/ribasim/input_base.py | 9 +++--- python/ribasim/tests/conftest.py | 5 +++ python/ribasim/tests/test_io.py | 23 ++++++++++++++ 5 files changed, 89 insertions(+), 34 deletions(-) diff --git a/docs/core/usage.qmd b/docs/core/usage.qmd index 1a2915196..92272053a 100644 --- a/docs/core/usage.qmd +++ b/docs/core/usage.qmd @@ -347,8 +347,8 @@ Lets a fraction (in [0,1]) of the incoming flow trough. column | type | unit | restriction ------------- | ------- | ------------ | ----------- node_id | Int | - | sorted +control_state | String | - | (optional) sorted per node_id fraction | Float64 | - | in the interval [0,1] -control_state | String | - | (optional) # TabulatedRatingCurve @@ -358,10 +358,10 @@ relation between the storage of a connected Basin (via the outlet level) and its column | type | unit | restriction ------------- | ------- | ------------ | ----------- node_id | Int | - | sorted +control_state | String | - | (optional) sorted per node_id active | Bool | - | (optional, default true) level | Float64 | $m$ | sorted per control_state discharge | Float64 | $m^3 s^{-1}$ | non-negative -control_state | String | - | (optional) sorted per node_id node_id | discharge | level ------- |----------- |------- @@ -381,8 +381,8 @@ Note that a `node_id` can be either in this table or in the static one, but not column | type | unit | restriction --------- | ------- | ------------ | ----------- -time | DateTime | - | sorted -node_id | Int | - | sorted per time +node_id | Int | - | sorted +time | DateTime | - | sorted per node_id level | Float64 | $m$ | - discharge | Float64 | $m^3 s^{-1}$ | non-negative @@ -397,11 +397,11 @@ When PID controlled, the pump must point away from the controlled basin in terms column | type | unit | restriction --------- | ------- | ------------ | ----------- node_id | Int | - | sorted +control_state | String | - | (optional) sorted per node_id active | Bool | - | (optional, default true) flow_rate | Float64 | $m^3 s^{-1}$ | non-negative min_flow_rate | Float64 | $m^3 s^{-1}$ | (optional, default 0.0) max_flow_rate | Float64 | $m^3 s^{-1}$ | (optional) -control_state | String | - | (optional) # Outlet @@ -411,12 +411,12 @@ When PID controlled, the outlet must point towards the controlled basin in terms column | type | unit | restriction --------- | ------- | ------------ | ----------- node_id | Int | - | sorted +control_state | String | - | (optional) sorted per node_id active | Bool | - | (optional, default true) flow_rate | Float64 | $m^3 s^{-1}$ | non-negative min_flow_rate | Float64 | $m^3 s^{-1}$ | (optional, default 0.0) max_flow_rate | Float64 | $m^3 s^{-1}$ | (optional) min_crest_level | Float64 | $m$ | (optional) -control_state | String | - | (optional) # User @@ -453,11 +453,11 @@ Note that a `node_id` can be either in this table or in the static one, but not column | type | unit | restriction ------------- | -------- | ------------ | ----------- node_id | Int | - | sorted +priority | Int | - | sorted per node id time | DateTime | - | sorted per priority per node id demand | Float64 | $m^3 s^{-1}$ | - return_factor | Float64 | - | between [0 - 1] min_level | Float64 | $m$ | (optional) -priority | Int | - | sorted per node id ## Allocation results @@ -502,8 +502,8 @@ Note that a `node_id` can be either in this table or in the static one, but not column | type | unit | restriction --------- | ------- | ------------ | ----------- -time | DateTime | - | sorted -node_id | Int | - | sorted per time +node_id | Int | - | sorted +time | DateTime | - | sorted per node_id level | Float64 | $m$ | - # FlowBoundary @@ -533,8 +533,8 @@ Note that a `node_id` can be either in this table or in the static one, but not column | type | unit | restriction --------- | ------- | ------------ | ----------- -time | DateTime | - | sorted -node_id | Int | - | sorted per time +node_id | Int | - | sorted +time | DateTime | - | sorted per node_id flow_rate | Float64 | $m^3 s^{-1}$ | non-negative # LinearResistance @@ -544,9 +544,9 @@ Flow proportional to the level difference between the connected basins. column | type | unit | restriction ------------- | ------- | ------------ | ----------- node_id | Int | - | sorted +control_state | String | - | (optional) sorted per node_id active | Bool | - | (optional, default true) resistance | Float64 | $sm^{-2}$ | - -control_state | String | - | (optional) # ManningResistance @@ -555,12 +555,12 @@ Flow through this connection is estimated by conservation of energy and the Mann column | type | unit | restriction ------------- | ------- | ------------ | ----------- node_id | Int | - | sorted +control_state | String | - | (optional) sorted per node_id active | Bool | - | (optional, default true) length | Float64 | $m$ | positive manning_n | Float64 | $s m^{-\frac{1}{3}}$ | positive profile_width | Float64 | $m$ | positive profile_slope | Float64 | - | - -control_state | String | - | (optional) # Terminal @@ -584,9 +584,9 @@ The condition schema defines conditions of the form 'the discrete_control node w column | type | unit | restriction ----------------- | -------- | ------- | ----------- node_id | Int | - | sorted -listen_feature_id | Int | - | - -variable | String | - | must be "level" or "flow_rate" -greater_than | Float64 | various | - +listen_feature_id | Int | - | sorted per node_id +variable | String | - | must be "level" or "flow_rate", sorted per listen_feature_id +greater_than | Float64 | various | sorted per variable look_ahead | Float64 | $s$ | Only on transient boundary conditions, non-negative (optional, default 0) ## DiscreteControl / logic @@ -595,8 +595,8 @@ The logic schema defines which control states are triggered based on the truth o DiscreteControl is applied in the Julia core as follows: - During the simulation it is checked whether the truth of any of the conditions changes. -- When a condition changes, the corresponding discrrete_control node id is retrieved (node_id in the condition schema above). -- The truth value of all the conditions this discrete_control node lisens to are retrieved, in the order as they are specified in the condition schema. This is then converted into a string of "T" for true and "F" for false. This string we call the truth state.* +- When a condition changes, the corresponding discrete_control node id is retrieved (node_id in the condition schema above). +- The truth value of all the conditions this discrete_control node listens to are retrieved, in the order as they are specified in the condition schema. This is then converted into a string of "T" for true and "F" for false. This string we call the truth state.* - The table below determines for the given discrete_control node ID and truth state what the corresponding control state is. - For all the nodes this discrete_control node affects (as given by the "control" edges in [Edges / static](usage.qmd#edge)), their parameters are set to those parameters in `NodeType / static` corresponding to the determined control state. @@ -605,8 +605,8 @@ DiscreteControl is applied in the Julia core as follows: column | type | unit | restriction -------------- | -------- | ---- | ----------- node_id | Int | - | sorted -truth_state | String | - | Consists of the characters "T" (true), "F" (false), "U" (upcrossing), "D" (downcrossing) and "*" (any) -control_state | String | - | +control_state | String | - | - +truth_state | String | - | Consists of the characters "T" (true), "F" (false), "U" (upcrossing), "D" (downcrossing) and "*" (any), sorted per node_id ## DiscreteControl results @@ -630,13 +630,13 @@ In the future controlling the flow on a particular edge could be supported. column | type | unit | restriction -------------- | -------- | -------- | ----------- node_id | Int | - | sorted +control_state | String | - | (optional) sorted per node_id active | Bool | - | (optional, default true) listen_node_id | Int | - | - target | Float64 | $m$ | - proportional | Float64 | $s^{-1}$ | - integral | Float64 | $s^{-2}$ | - derivative | Float64 | - | - -control_state | String | - | - ## PidControl / time @@ -650,8 +650,8 @@ Note that a `node_id` can be either in this table or in the static one, but not column | type | unit | restriction -------------- | -------- | -------- | ----------- -node_id | Int | - | sorted per time -time | DateTime | - | sorted +node_id | Int | - | sorted +time | DateTime | - | sorted per node_id listen_node_id | Int | - | - target | Float64 | $m$ | - proportional | Float64 | $s^{-1}$ | - diff --git a/python/ribasim/ribasim/config.py b/python/ribasim/ribasim/config.py index ca8983d5f..e992e811b 100644 --- a/python/ribasim/ribasim/config.py +++ b/python/ribasim/ribasim/config.py @@ -82,6 +82,8 @@ class Terminal(NodeModel): default_factory=TableModel[TerminalStaticSchema] ) + _sort_keys: dict[str, list[str]] = {"static": ["node_id"]} + class PidControl(NodeModel): static: TableModel[PidControlStaticSchema] = Field( @@ -91,7 +93,10 @@ class PidControl(NodeModel): default_factory=TableModel[PidControlTimeSchema] ) - _sort_keys: dict[str, list[str]] = {"time": ["time", "node_id"]} + _sort_keys: dict[str, list[str]] = { + "static": ["node_id", "control_state"], + "time": ["node_id", "time"], + } class LevelBoundary(NodeModel): @@ -102,7 +107,10 @@ class LevelBoundary(NodeModel): default_factory=TableModel[LevelBoundaryTimeSchema] ) - _sort_keys: dict[str, list[str]] = {"time": ["time", "node_id"]} + _sort_keys: dict[str, list[str]] = { + "static": ["node_id"], + "time": ["node_id", "time"], + } class Pump(NodeModel): @@ -110,6 +118,8 @@ class Pump(NodeModel): default_factory=TableModel[PumpStaticSchema] ) + _sort_keys: dict[str, list[str]] = {"static": ["node_id", "control_state"]} + class TabulatedRatingCurve(NodeModel): static: TableModel[TabulatedRatingCurveStaticSchema] = Field( @@ -119,8 +129,8 @@ class TabulatedRatingCurve(NodeModel): default_factory=TableModel[TabulatedRatingCurveTimeSchema] ) _sort_keys: dict[str, list[str]] = { - "static": ["node_id", "level"], - "time": ["time", "node_id", "level"], + "static": ["node_id", "control_state", "level"], + "time": ["node_id", "time", "level"], } @@ -144,7 +154,10 @@ class FlowBoundary(NodeModel): default_factory=TableModel[FlowBoundaryTimeSchema] ) - _sort_keys: dict[str, list[str]] = {"time": ["time", "node_id"]} + _sort_keys: dict[str, list[str]] = { + "static": ["node_id"], + "time": ["node_id", "time"], + } class Basin(NodeModel): @@ -165,8 +178,10 @@ class Basin(NodeModel): ) _sort_keys: dict[str, list[str]] = { + "static": ["node_id"], + "state": ["node_id"], "profile": ["node_id", "level"], - "time": ["time", "node_id"], + "time": ["node_id", "time"], "subgrid": ["subgrid_id", "basin_level"], } @@ -176,6 +191,8 @@ class ManningResistance(NodeModel): default_factory=TableModel[ManningResistanceStaticSchema] ) + _sort_keys: dict[str, list[str]] = {"static": ["node_id", "control_state"]} + class DiscreteControl(NodeModel): condition: TableModel[DiscreteControlConditionSchema] = Field( @@ -185,20 +202,31 @@ class DiscreteControl(NodeModel): default_factory=TableModel[DiscreteControlLogicSchema] ) + _sort_keys: dict[str, list[str]] = { + "condition": ["node_id", "listen_feature_id", "variable", "greater_than"], + "logic": ["node_id", "truth_state"], + } + class Outlet(NodeModel): static: TableModel[OutletStaticSchema] = Field( default_factory=TableModel[OutletStaticSchema] ) + _sort_keys: dict[str, list[str]] = {"static": ["node_id", "control_state"]} + class LinearResistance(NodeModel): static: TableModel[LinearResistanceStaticSchema] = Field( default_factory=TableModel[LinearResistanceStaticSchema] ) + _sort_keys: dict[str, list[str]] = {"static": ["node_id", "control_state"]} + class FractionalFlow(NodeModel): static: TableModel[FractionalFlowStaticSchema] = Field( default_factory=TableModel[FractionalFlowStaticSchema] ) + + _sort_keys: dict[str, list[str]] = {"static": ["node_id", "control_state"]} diff --git a/python/ribasim/ribasim/input_base.py b/python/ribasim/ribasim/input_base.py index f9aadb3b5..1538bfafa 100644 --- a/python/ribasim/ribasim/input_base.py +++ b/python/ribasim/ribasim/input_base.py @@ -289,10 +289,9 @@ def _from_arrow(cls, path: FilePath) -> pd.DataFrame: directory = context_file_loading.get().get("directory", Path(".")) return pd.read_feather(directory / path) - def sort(self, sort_keys: list[str] = ["node_id"]): - """Sort all input tables as required. + def sort(self, sort_keys: list[str]): + """Sort the table as required. - Tables are sorted by "node_id", unless otherwise specified. Sorting is done automatically before writing the table. """ if self.df is not None: @@ -375,7 +374,7 @@ def _write_table(self, path: FilePath) -> None: gdf.to_file(path, layer=self.tablename(), driver="GPKG") - def sort(self, sort_keys: list[str] = ["node_id"]): + def sort(self, sort_keys: list[str]): self.df.sort_index(inplace=True) @@ -435,7 +434,7 @@ def _save(self, directory: DirectoryPath, input_dir: DirectoryPath, **kwargs): getattr(self, field)._save( directory, input_dir, - sort_keys=self._sort_keys.get("field", ["node_id"]), + sort_keys=self._sort_keys[field], ) def _repr_content(self) -> str: diff --git a/python/ribasim/tests/conftest.py b/python/ribasim/tests/conftest.py index 4e4c1d09f..f6dbb730d 100644 --- a/python/ribasim/tests/conftest.py +++ b/python/ribasim/tests/conftest.py @@ -32,3 +32,8 @@ def backwater() -> ribasim.Model: @pytest.fixture() def discrete_control_of_pid_control() -> ribasim.Model: return ribasim_testmodels.discrete_control_of_pid_control_model() + + +@pytest.fixture() +def level_setpoint_with_minmax() -> ribasim.Model: + return ribasim_testmodels.level_setpoint_with_minmax_model() diff --git a/python/ribasim/tests/test_io.py b/python/ribasim/tests/test_io.py index 888c692f8..b1ac52056 100644 --- a/python/ribasim/tests/test_io.py +++ b/python/ribasim/tests/test_io.py @@ -102,3 +102,26 @@ def test_extra_columns(basic_transient): node = Node(df=df) assert "meta_node_id" in node.df.columns + + +def test_sort(level_setpoint_with_minmax, tmp_path): + model = level_setpoint_with_minmax + table = model.discrete_control.condition + + # apply a wrong sort, then call the sort method to restore order + table.df.sort_values("greater_than", ascending=False, inplace=True) + assert table.df.iloc[0]["greater_than"] == 15.0 + sort_keys = model.discrete_control._sort_keys["condition"] + assert sort_keys == ["node_id", "listen_feature_id", "variable", "greater_than"] + table.sort(sort_keys) + assert table.df.iloc[0]["greater_than"] == 5.0 + + # re-apply wrong sort, then check if it gets sorted on write + table.df.sort_values("greater_than", ascending=False, inplace=True) + model.write(tmp_path / "basic/ribasim.toml") + # write sorts the model in place + assert table.df.iloc[0]["greater_than"] == 5.0 + model_loaded = ribasim.Model(filepath=tmp_path / "basic/ribasim.toml") + table_loaded = model_loaded.discrete_control.condition + assert table_loaded.df.iloc[0]["greater_than"] == 5.0 + __assert_equal(table.df, table_loaded.df) From b09373c5abc2ddb3685060be3617aef46579a3ac Mon Sep 17 00:00:00 2001 From: Martijn Visser Date: Mon, 15 Jan 2024 18:44:27 +0100 Subject: [PATCH 09/82] Pixi: use latest QGIS release (#958) I tried `pixi run qgis`, which up to now was set to the LTS release, and it was broken on loading the plugin: ``` Windows fatal exception: access violation Current thread 0x00006700 (most recent call first): File "C:\Users/visser_mn/AppData/Roaming/QGIS/QGIS3\profiles\default/python/plugins\ribasim_qgis\widgets\ribasim_widget.py", line 47 in __init__ self.tabwidget.addTab(self.__dataset_widget, "Model") File "C:\Users/visser_mn/AppData/Roaming/QGIS/QGIS3\profiles\default/python/plugins\ribasim_qgis\ribasim_qgis.py", line 48 in toggle_ribasim widget = RibasimWidget(self.ribasim_widget, self.iface) ``` I saw this happens on 3.28.12, which is the last LTS in conda-forge, but locally my OSGeo4w qgis-ltr release is 3.28.14, which doesn't have this issue. I propose we switch to the latest QGIS release, which fixes this. In pixi we set QGIS to the LTS since that is the oldest we support, but this is the only dependency for which we set it to the oldest version. And also it holds a lot of other dependencies in our environment back as can be seen from the size of the diff. If we want to check the oldest supported QGIS release we can perhaps use https://pixi.sh/design_proposals/multi_environment_proposal/ in the future for this, same as for Python versions. --- pixi.lock | 9459 +++++++++++++++++++++++++---------------------------- pixi.toml | 2 +- 2 files changed, 4439 insertions(+), 5022 deletions(-) diff --git a/pixi.lock b/pixi.lock index 0e765a511..d9ecf8b92 100644 --- a/pixi.lock +++ b/pixi.lock @@ -60,23 +60,23 @@ package: timestamp: 1650670423406 - platform: linux-64 name: alsa-lib - version: 1.2.9 + version: 1.2.10 category: main manager: conda dependencies: - libgcc-ng >=12 - url: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.9-hd590300_0.conda + url: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.10-hd590300_0.conda hash: - md5: a0c6f0e7e1a467f5678f94dea18c8aa7 - sha256: f177627acdfcead15a28f4a07fcda6a1e26b83f053eaa1efa7cce01c0a3b09a8 + md5: 75dae9a4201732aa78a530b826ee5fe0 + sha256: 51147922bad9d3176e780eb26f748f380cd3184896a9f9125d8ac64fe330158b build: hd590300_0 arch: x86_64 subdir: linux-64 build_number: 0 license: LGPL-2.1-or-later license_family: GPL - 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- pkg:pypi/zipp - platform: linux-64 name: zlib version: 1.2.13 diff --git a/pixi.toml b/pixi.toml index 356e51e51..f3cea5339 100644 --- a/pixi.toml +++ b/pixi.toml @@ -139,7 +139,7 @@ pytest = "*" pytest-cov = "*" pytest-xdist = "*" python = ">=3.10" -qgis = "3.28.*" +qgis = "*" qgis-plugin-manager = "*" quartodoc = "*" ruff = "*" From 0102b02c814b6b16e8c1c38c1aab9dc41000726c Mon Sep 17 00:00:00 2001 From: Huite Date: Tue, 16 Jan 2024 11:52:53 +0100 Subject: [PATCH 10/82] Docs additions for output, logging, and metadata (#961) Fixes #945 Fixes #950 --- docs/core/usage.qmd | 34 +++++++++++++++++++++++++++++++++- 1 file changed, 33 insertions(+), 1 deletion(-) diff --git a/docs/core/usage.qmd b/docs/core/usage.qmd index 92272053a..e8e2789bd 100644 --- a/docs/core/usage.qmd +++ b/docs/core/usage.qmd @@ -70,6 +70,25 @@ Currently there are the following allocation settings: - `use_allocation`: A boolean which says whether allocation should be used or not; - `timestep`: a float value in seconds which dictates the update interval for allocations. +## Results settings + +The following entries can be set in the configuration in the `[results]` section. + +entry | type | description +----------------- | ------ | ----------- +compression | String | Compression algorithm: zstd or lz4. +compression_level | Int | Compression level. Higher is more compression. +subgrid | Bool | Compute and output more detailed water levels. + +## Logging settings + +The following entries can be set in the configuration in the `[logging]` section. + +entry | type | description +----------------- | ------ | ----------- +verbosity | String | Verbosity level: debug, info, warn, or error. +timing | Bool | Enable timings. + # GeoPackage database and Arrow tables The input and output tables described below all share that they are tabular files. The Node @@ -95,6 +114,8 @@ apply [dictionary encoding](https://arrow.apache.org/docs/format/Columnar.html#dictionary-encoded-layout) to those columns. +## Table requirements + Below we give details per file, in which we describe the schema of the table using a syntax like this: @@ -112,7 +133,18 @@ Tables are also allowed to have rows for timestamps that are not part of the sim these will be ignored. That makes it easy to prepare data for a larger period, and test models on a shorted period. -When preparing the model for simulation, input validation is performed in the Julia core. The validation rules are described in the [validation](validation.qmd) section. +When preparing the model for simulation, input validation is performed in the Julia core. +The validation rules are described in the [validation](validation.qmd) section. + +## Custom metadata + +It may be advantageous to add metadata to rows. For example, basin areas might have names and +objects such as weirs might have specific identification codes. Additional columns can be freely +added to tables. The column names should be prefixed with `meta_`. They will not be used in +computations or validated by the Julia core. + +The ribasim-python library will automatically add the `meta_` prefix to non-standard columns. +Column names already prefixed with `meta_` will not be updated. # Node From 94ef9ada9f2a30e1976c896aedfa371f400dd463 Mon Sep 17 00:00:00 2001 From: Hofer-Julian <30049909+Hofer-Julian@users.noreply.github.com> Date: Tue, 16 Jan 2024 13:39:52 +0100 Subject: [PATCH 11/82] Remove coupling docs (#963) They now live at https://deltares.github.io/iMOD-Documentation/coupler_ribamod_config.html --- docs/_quarto.yml | 7 - docs/core/index.qmd | 6 + docs/couple/index.qmd | 19 -- docs/couple/modflow-demo.qmd | 239 ------------------------- docs/couple/modflow.qmd | 338 ----------------------------------- 5 files changed, 6 insertions(+), 603 deletions(-) delete mode 100644 docs/couple/index.qmd delete mode 100644 docs/couple/modflow-demo.qmd delete mode 100644 docs/couple/modflow.qmd diff --git a/docs/_quarto.yml b/docs/_quarto.yml index a29c13c49..9be70ea44 100644 --- a/docs/_quarto.yml +++ b/docs/_quarto.yml @@ -15,8 +15,6 @@ website: file: python/index.qmd - text: "QGIS plugin" file: qgis/index.qmd - - text: "Coupled models" - file: couple/index.qmd - text: "Contributing" file: contribute/index.qmd right: @@ -40,11 +38,6 @@ website: - python/examples.ipynb - python/reference/index.qmd - python/test-models.qmd - - title: "Coupled models" - contents: - - couple/index.qmd - - couple/modflow.qmd - - couple/modflow-demo.qmd - title: "Contributing" contents: - contribute/index.qmd diff --git a/docs/core/index.qmd b/docs/core/index.qmd index 775ad346b..55a864059 100644 --- a/docs/core/index.qmd +++ b/docs/core/index.qmd @@ -37,3 +37,9 @@ Sim --> Finished Finished -->|no| Con Finished -->|yes| Done ``` + + +# Coupling + +Ribasim can also be coupled to other kernels with the help of iMOD Coupler. +The corresponding documentation can be found within the [iMOD Suite Documentation](https://deltares.github.io/iMOD-Documentation/coupler.html). diff --git a/docs/couple/index.qmd b/docs/couple/index.qmd deleted file mode 100644 index 68457e287..000000000 --- a/docs/couple/index.qmd +++ /dev/null @@ -1,19 +0,0 @@ ---- -title: "Coupled models" ---- - -Ribasim can be coupled to other software, for instance to model another process or domain, -or to control a simulation from another process. - -To enable this, Ribasim can be compiled as a shared library (`libribasim`) instead of a -command line interface (`ribasim`). This shared library exposes a C API in the form of the -[Basic Model Interface](https://bmi.readthedocs.io/) (BMI). Other software can then load -`libribasim` and load a Ribasim model, exchange data, and control the time stepping. - -An initial coupling to MODFLOW 6 was done in 2022 inside the [Julia core](../core/) as a -proof of concept. Read about the [coupling setup](modflow.qmd) and see the -[demonstration](modflow-demo.qmd). Going forward this and other coupling codes will be -implemented outside of the core, by making use of -[iMOD Coupler](https://deltares.github.io/iMOD-Documentation/coupler_index.html) and -`libribasim`. iMOD Coupler is a generic coupling tool, and can be used to couple to other -models as well. diff --git a/docs/couple/modflow-demo.qmd b/docs/couple/modflow-demo.qmd deleted file mode 100644 index 628532baf..000000000 --- a/docs/couple/modflow-demo.qmd +++ /dev/null @@ -1,239 +0,0 @@ ---- -title: "MODFLOW 6 Demonstration" ---- - -## Example: parametrization - -In our test cases, we will work with the Dutch national groundwater model -(LHM). For testing, we simplify the top boundary conditions to just three -surface water "systems", from large to small: - -1. Primary -2. Secondary -3. Tertiary - -These systems are separated in the groundwater model schematization due to the -relatively small size of the surface waters (several meters in width) in -comparison with relatively coarse cells of the groundwater model (250 m): most -cells in the LHM contain more than one surface water, and are included via -representative parameters which take the physical scaling into account. In case -of sufficiently small cell sizes, no overlap occurs and all surface waters can -be represented in a single grid. - -Ribasim has no knowledge of these systems unless explicitly separated into -different (sub-)basins. In the examples below, these three systems are -represented by one basin with a single volume. For the purposes of testing, we -have not yet created empirical volume-level relationships for the surface water -of every cell extracted from a hydraulic model. Instead, we have chosen an -(over)simplified parametrization of the hydraulic properties, which makes it -easy to verify the behavior of Ribasim and the coupling procedures: - -1. Primary, secondary, and tertiary systems have a rectangular profile: the - area of the surface water does not change with water level or volume. -2. Water depth is constant for a system within a basin. -3. Water depth increases linearly with volume. (This follows from 1.) -4. Water depth is distributed across the systems in a geometric progression: - when the tertiary system contains 0.1 m of water, the secondary system contains -0.2 m, and the primary system contains 0.4 m. -5. Water depth is 0.0 m for all systems when basin volume is 0.0. (This follows from 4.) -6. The distribution of water occurs according to the surface water area (width - times length) used for the LHM parametrization of river bed conductance. - -For freely draining basins, a simplified storage-discharge relationship has -been derived as follows: - -1. The area of the basin polygon has been multiplied by 1 mm/d (roughly the -average precipitation excess in the Netherlands). This yields a "normative -discharge". -2. A corresponding normative volume has been chosen, corresponding with water -depths of 0.4, 0.2, and 0.1 m for the primary, secondary, and tertiary surface -waters respectively. -3. A dead storage volume has been chosen, corresponding with water depths of -0.2, 0.1, and 0.05 m for the primary, secondary, and tertiary surface waters -respectively. The basin only starts discharging when the storage volume exceeds -this value. - -:::{.callout-note} -Ribasim is not limited to such oversimplified parametrization! Ribasim uses -tabulations and therefore supports arbitrary (piecewise linear) volume-depth -and volume-discharge relationships. -::: - -A visual representation of this simplified conceptual schematization is given -in @fig-volume-depth and @fig-volume-discharge. - -![Distribution of water depths over the primary, secondary, and tertiary system.](https://user-images.githubusercontent.com/13662783/187665858-d01fd60f-f3c2-4662-af82-cf8acfbe169b.PNG){#fig-volume-depth} - -![Discharge as a function of basin storage volume.](https://user-images.githubusercontent.com/13662783/187668931-c04d4126-9208-44f5-bafa-4c5f74a96dc9.PNG){#fig-volume-discharge} - -An example of the resulting parameters for a single cell is shown in -@tbl-hupsel-v-h. The first row shows the water levels when the basin is empty. -The level for primary, secondary, and tertiary are equal to the bottom -elevation of the surface waters. The second row shows the volume and levels for -water depths of 0.4, 0.2, and 0.1 m. The third row shows the volume and levels -for a tenfold larger volume. This results in implausible water levels with -depths of 4.0, 2.0 and 1.0 m; the water level in the primary system is over -two meters higher than in the tertiary system. In reality, the surface waters -would overflow and surface ponding would occur; this mechanism is ignored -in the test cases for the sake of simplicity. - -| Volume (m3) | Primary (m NAP) | Secondary (m NAP) | Tertiary (m NAP) | -|-------------|-----------------|-------------------|------------------| -| 0.0 | 25.65 | 25.83 | 26.60 | -| 6843.1 | 26.05 | 26.03 | 26.70 | -| 68431.0 | 29.65 | 27.83 | 27.60 | - -: Volume-level table for a single cell in the Hupsel basin. {#tbl-hupsel-v-h} - -@fig-grid-volume shows the volume of the first row of the cell based -input for the primary system. Symbology is set to unique values. While water -levels differ per cell in this parametrization, the "normative volume" defined -above is shared by all cells in a basin. - -![Basin normative volume of the primary system.](https://user-images.githubusercontent.com/13662783/187672671-20d22031-3b50-474a-9ee1-4408c25a4f30.PNG){#fig-grid-volume} - -@fig-grid-volume shows the water level corresponding to the normative storage -volume based input for the primary system (it corresponds to the value shown in -the first row of the primary column in @tbl-hupsel-v-h). We see a clear gradient -from west to east: as our simplified parametrization assumes a constant water -depth for all cells in a single system, water levels spatially fall and rise -with the bottom elevation. - -![Water level corresponding to the normative basin volume of the primary system.](https://user-images.githubusercontent.com/13662783/187672663-99b9efd3-5e09-4d6f-bd3a-4180ff5b2ce4.PNG){#fig-grid-level} - -## Example: Configuration - -An example of the MODFLOW 6 section of TOML configuration required for a coupled -run can be seen below: - -```TOML -[modflow] -simulation = "../data/hupsel/mfsim.nam" -mode = "sequential" -timestep = 86400.0 - -[modflow.models] - -[modflow.models.gwf] -type = "gwf" -dataset = "../data/volume_level_profile-hupsel.nc" -basins = "basin_id" - -[[modflow.models.gwf.bounds]] -river = "RIV_P" -drain = "DRN_P" -profile = "profile_primary" - -[[modflow.models.gwf.bounds]] -river = "RIV_S" -drain = "DRN_S" -profile = "profile_secondary" - -[[modflow.models.gwf.bounds]] -drain = "DRN_T" -profile = "profile_tertiary" -``` - -The section starts by stating the path to the MODFLOW 6 simulation name file -(`simulation`). The next section contains the information regarding the -MODFLOW 6 model(s) to couple to Ribasim's basins. Per model, a path to the coupling -parameter dataset is provided (`dataset`), along with the variable to use as -the basin identification number (`basins`). Next, for every boundary condition -that should be coupled to Ribasim, the package names (`river`, `drain`) used by -MODFLOW 6 must be specified (as we look for these names in the MODFLOW 6 memory), -along with the name of the variable in the coupling dataset which provides the -volume-level relationship (`profile`). - -As can be seen in the example, the coupling mechanism supports coupling of: - -1. A single drainage package (`drain` entry). -2. A single river package (`river` entry). -3. A combination of river and drainage package (when infiltration conductance -does not equal drainage conductance) both (`river` and `drain` entry). - -## Test case: Hupsel - -To test the coupling, the following simulations have been setup and run: - -1. A standalone MODFLOW 6 run of sequential steady-states (i.e. no storage) with -differing groundwater recharge values. -2. A coupled run where the MODFLOW 6 stages are updated by the Ribasim coupler -process, but without Ribasim. This results in volumes of 0.0, so all MODFLOW 6 -water levels are set equal to bed elevation. -3. A coupled run where the water levels are updated by Ribasim. - -From these tests, we expect the following behavior: - -1. Drainage terms should remain largely the same when the water level is lowered in a steady-state: - the amount of recharge is fixed, and this is locally drained. -2. In case of negative recharge (evapotranspiration), infiltration occurs in the surface waters. - Infiltration should be zero when the basin volume is 0. - -![Water balance of the MODFLOW 6 boundary conditions for the Hupsel basin for a standalone MODFLOW 6 run. The four sequential steady states (01, 02, 03, 04) use net groundwater recharge values of 1.0, 0.5, -0.05 and -0.1 mm/d.](https://user-images.githubusercontent.com/13662783/187715341-fd99dc06-2eda-4b84-a201-650dc7220574.png){#fig-hupsel-gwb-steady} - -@fig-hupsel-gwb-steady shows the water balance of steady-state for submodel of the -LHM that has been by selecting the cells belonging to the district containing -the Hupsel catch, the Berkel. - -The Hupsel basin show the expected behavior: for a net groundwater recharge of -1.0 mm/d, most is precipitation with a minor part lateral inflow from higher -areas. In terms of outgoing flows, most of the precipitation ends up in the -surface water, primarily in the many ditches of the tertiary system. Only a -relatively small part of the water leaves the basin via the groundwater. -Interbasin flows through the groundwater form such a minor role, as the aquifer -is thin and transmissivity is limited. - -Reducing groundwater recharge to 0.5 mm/d reduces all flows, with the tertiary -system playing a less dominant role, relatively speaking: as its elevation is -the highest compared to the primary and secondary system, the head difference -is reduced strongest for the tertiary system. - -With evapotranspiration (ET) excess (-0.05 and 0.1 mm/d; low values are chosen here -since most ET would be drawn from storage, which is not available in a -steady-state model), the surface waters provide mostly inflow, and recharge is -a negative term. In this case, the secondary system provides a small amount of -infiltration; most of the water is drawn from the surroundings instead. - -![Water balance of the MODFLOW 6 boundary conditions for the Hupsel basin for a zero volume run. The four sequential steady states (01, 02, 03, 04) use net groundwater recharge values of 1.0, 0.5, -0.05 and -0.1 mm/d.](https://user-images.githubusercontent.com/13662783/187715349-9eee8830-9b03-4a88-b7c9-b16004c694f6.png){#fig-hupsel-gwb-volume0} - -@fig-hupsel-gwb-volume0 shows the same model, with 0-basin volume which causes -water levels to be set equal to bed elevation. Consequently, primary and -secondary outflow terms are larger for positive groundwater recharge as they -drain at a lower level and intercept the water before the tertiary system does. -Secondly, with negative groundwater recharge, no infiltration occurs and the -water is drawn from the surroundings instead. This shows the coupling mechanism -adjusting MODFLOW 6 water levels successfully. - -## Test case: de Tol - -To test the coupling, the following simulations have been setup and run: - -1. A standalone MODFLOW 6 run of sequential steady-states (i.e. no storage) with -differing groundwater recharge values. -2. A coupled run where the MODFLOW 6 stages are updated by the Ribasim coupler -process, but without Ribasim. This results in volumes of 0.0, so all MODFLOW 6 -water levels are set equal to bed elevation. -3. A coupled run where the water levels are updated by Ribasim. - -![Water balance of the MODFLOW 6 boundary conditions for De Tol basin for a standalone MODFLOW 6 run. The four sequential steady states (01, 02, 03, 04) use net groundwater recharge values of 1.0, 0.5, -0.05 and -0.1 mm/d.](https://user-images.githubusercontent.com/13662783/187769185-f63a5821-dfe8-4d99-b43e-780962e73870.png){#fig-tol-gwb-steady} - -@fig-tol-gwb-steady shows the water balance of steady-state for a submodel of -the LHM for the Polder de Tol and its surroundings. While groundwater recharge -is the dominant ingoing flow, lateral groundwater flow (over the entire depth -of the groundwater model) is a sizable inflow for the area; the larger lateral -inflow shows that De Tol is a net receiver of groundwater which is mostly -discharged through the secondary system. In contrast to the Hupsel, the -tertiary system is almost entirely absent: drainage occurs not through -ephemeral tertiary ditches, but by the permanently water-bearing ditches of the -primary and secondary system. Unlike the Hupsel, the water balance does not -shrink to very small discharges, as there is sizable regional groundwater flow. - -![Water balance of the MODFLOW 6 boundary conditions for De Tol basin for a zero volume run. The four sequential steady states (01, 02, 03, 04) use net groundwater recharge values of 1.0, 0.5, -0.05 and -0.1 mm/d.](https://user-images.githubusercontent.com/13662783/187769180-91f6344c-3489-4200-8a0c-d5e82a28ebaf.png){#fig-tol-gwb-volume0} - -@fig-tol-gwb-volume0 shows the same model, with 0-basin volume which causes -water levels to be set equal to bed elevation. The total discharge is larger: -the primary and secondary systems are set to lower levels, and so the head -difference is larger. While De Tol's evapotranspiration excess can be fed by -the regional groundwater, the primary and secondary ditches also provide some -part; as expected, they do not feed when the coupling mechanism adjusts -MODFLOW 6's water levels. diff --git a/docs/couple/modflow.qmd b/docs/couple/modflow.qmd deleted file mode 100644 index 60862bbcc..000000000 --- a/docs/couple/modflow.qmd +++ /dev/null @@ -1,338 +0,0 @@ ---- -title: "MODFLOW 6" ---- - -Ribasim has been designed to provide a computationally efficient representation of -surface water for MODFLOW 6. It does so by connecting to basic MODFLOW 6 boundary -conditions: the river and drainage packages. - -Ribasim connects to MODFLOW 6 via the Basic Model Interface (BMI) and Extended -Model Interface (XMI) [@hughes2022modflow]. BMI describes the interface to -initialize a model, get values from its memory, run a timestep, etc. XMI -extends this interface to allow much finer control into MODFLOW 6's solution -procedures. We have written a Julia package [@modflowinterface] which -implements this interface for the Julia programming language. In coupling, Ribasim -uses this interface to get the head values, the boundary condition water -levels, and the budgets term of the MODFLOW 6 groundwater model while MODFLOW 6 -is running. - -Additionally, links can be made with other (BMI/XMI-compliant) processes and -models. One example of such a link is using the surface runoff and the -agricultural irrigation demand calculated by an unsaturated zone model; in the -Netherlands Hydrological Instrument MetaSWAP provides this demand. - -# MODFLOW Concepts -## Drainage - -The drainage package can be simulated to agricultural drains, ditches, or -draining streams. The amount of water removed from the aquifer is proportional -to the difference between the groundwater head and the drainage elevation. -Drainage only occurs when the head is larger than the elevation; this boundary -condition does not allow infiltration into the groundwater. - -$$ -Q_{drain} = \left\{ - \begin{array}{ c l } - C_{drain} (\phi - h_{drain}) & \quad \textrm{if } \phi > h_{drain} \\ - 0 & \quad \textrm{otherwise} - \end{array} -\right. -$$ - -## River - -The river package can both drain the groundwater, or infiltrate surface water -to the groundwater. It limits the amount of water that can infiltrate when -the groundwater head falls below the river bottom, in which cases it assumes -atmospheric pressure conditions underneath the surface water. - -$$ -Q_{river} = \left\{ - \begin{array}{ c l } - C_{river} (\phi - h_{river}) & \quad \textrm{if } \phi > b_{river} \\ - C_{river} (h_{river} - b_{river}) & \quad \textrm{if } \phi <= b_{river} - \end{array} -\right. -$$ - -In the Netherlands, it is somewhat common to make a distinction between the -drainage and infiltration conductance of surface waters. Drainage conductance -is often larger than the infiltration conductance due to clogging processes, -seepage through sides of the ditches, less contracted flow lines, etc. - -$$ -Q_{river} = \left\{ - \begin{array}{ c l } - C_{river,drn} (\phi - h_{river}) & \quad \textrm{if } \phi > h_{river} \\ - C_{river,inf} (\phi - h_{river}) & \quad \textrm{if } \phi <= h_{river} \\ - C_{river,inf} (h_{river} - b_{river}) & \quad \textrm{if } \phi <= b_{river} - \end{array} -\right. -$$ - -MODFLOW 6 does not support this (currently), but an identical effect may be -achieved by "stacking" a drainage package on top of a river package with these -values: - -$$ -\begin{array}{ c l } - h_{drain} = h_{river} \\ - C_{drain} = C_{river,drn} - C_{river,inf} -\end{array} -$$ - -# Coupling - -Broadly speaking, three schemes are commonly considered for coupling -hydrological kernels [@vanwalsum2011integration], [@hughes2012documentation]: - -1. Sequential: the first model computes a timestep and calculates a state or flux. -This is passed on to the second model, which then computes its timestep. -2. Iterative: the first model computes a timestep and calculates a state or -flux. This is passed on to the second models, which computes its timestep. This -results in an updated boundary condition for the first model, which recomputes -the timestep, then the second model recomputes its timestep, etc. These -iterations are repeated until some convergence criteria are met. -3. Fully coupled: all equations (e.g. the governing equations of both -groundwater flow and surface water flow) are solved at the same time. - -Each scheme has its advantages and disadvantages. Numerically speaking, the -fully coupled approach is most robust, but it effectively means a single -all-encompassing hydrological kernel. The first scheme is computationally the -cheapest, but states and fluxes lag one timestep behind, so that mass -conservation is not guaranteed. For example, based on its river levels, -MODFLOW 6 may compute a infiltration flux. Ribasim then runs its timestep, and -finds that given MODFLOW 6's infiltration flux, no water is present in the -surface waters: the infiltration flux has been overestimated by MODFLOW 6, and -mass is not conserved. - -Such an error is avoided in the second scheme: states and fluxes only lag a -single iteration behind, and the iterations are repeated until the difference -is negligible. Taking the example from above, the emptying of the surface -waters would result in lower water levels and recuded infiltration in the -second iteration. Mass is conserved, but at a higher computational cost. - -Currently, we have only implemented the sequential scheme for coupling Ribasim to -MODFLOW 6. However, the iterative solution is relatively easy to implement: it -is in essence a repeated sequential step. - -## Numerical solution in MODFLOW - -MODFLOW uses a backward-in-time implicit solution scheme. This creates a large -system of equations (a water balance for every cell), which it solves by -repeatedly solving a linearized system of equations instead. In matrix form, -this system of equations is expressed by: - -$$ -\mathbf{Ax} = \mathbf{b} -$$ - -Where $\mathbf{x}$ is a vector containing the head of every cell. - -For the boundary conditions, this requires linearization of the flow equations. -Flow from outside of the aquifer (cell) may be represented by: - -$$ -a = p\phi + q -$$ - -(Equation 2-6 in the MODFLOW 6 documentation [@langevin2017documentation].) - -For e.g. a draining boundary condition, the flow is head dependent: - -$$ -a = C(h - \phi) = -C\phi + Ch -$$ - -With $C$ the conductance, $h$ the boundary head or elevation, and $\phi$ -the groundwater head. - -In MODFLOW's internal formulation, the term in $\mathbf{A}$ is called -"coefficient of head" or hcof. Terms in $\mathbf{b}$ are called "right hand -side" or rhs. We can separate the equation above: - -$$ -\begin{aligned} -p = \text{hcof} = -C \\ -q = \textrm{rhs} = -Ch \\ -a = -C\phi + Ch = \text{hcof} * \phi - \text{rhs} -\end{aligned} -$$ - -For every boundary condition, MODFLOW 6 stores the `hcof` and `rhs` values. This -makes it quite convenient for us to compute the water budget for every boundary -condition: we simply multiply the hcof value by the head of the cell and -subtract the rhs. - -Note that hcof may have a value of 0! For example, when for a river boundary -the $\phi <= b_{river}$ condition occurs, the flow into the cell is -controlled only by $h_{river}$ and $b_{river}$ (equal to recharge for the -linear solution). - -## Sequential coupled solution - -A coupled run stars by initializing both models and creating the exchange -information: which MODFLOW 6 boundary condition is connected to which Ribasim -basin. While the model is running, the model proceeds through time as follows: - -1. Ribasim solves the equations on a basin level; this occurs with adaptive -timestepping via ModelingToolkit. -2. At a specified time (in accordance with the MODFLOW 6 time discretization), -the volumes are converted to MODFLOW 6 boundary condition levels using a -Callback function. -3. MODFLOW 6 runs a timestep. -4. The drainage and infiltration budgets are computed from MODFLOW 6 using the -equations described above and aggregated per basin. -5. The aggregated values are set as Ribasim boundary conditions, and Ribasim -solves until the next preset exchange time. - -These steps run until the final timestep is finished. - -## Iterative coupled solution - -:::{.callout-note} -We have not implemented an iterative coupled solution yet. The section below -describes an approach. -::: - -The simplest form of a iterative solution occurs as follows: - -1. MODFLOW 6 computes drainage and infiltration flows. -2. Ribasim uses these flows to compute a storage volume for the basin. -3. The volume is translated to a water level for every MODFLOW 6 boundary -condition in the basins. -4. MODFLOW 6 recomputes drainage and infiltration flows with the updated water -levels, etc. - -Such a scheme is not maximally efficient: the discharge and infiltration terms -are not constant, but are driven by a head difference. This head difference -depends on the level of the boundary conditions and head of every cell of the -groundwater model. If the surface waters of a basin empty, the water level will -decrease and drainage and infiltration flows will change. Ideally, we can -provide Ribasim with more information, so that it may estimate drainage and -infiltration terms better. - -As groundwater flow is often (approximately) linear, we can use linearization -to more efficiently compute the flow from Ribasim's side as well. In the iterative -coupled solution, we are solving both MODFLOW 6 and Ribasim repeatedly, until they -produce same drainage or infiltration (approximately). One of Ribasim's basins -contains many MODFLOW cells with boundary conditions. We could add every -boundary condition to Ribasim's equations, but this is costly and cumbersome. -Fortunately, linearization allows us to "stack" (superpose) all the different -boundary conditions into a single, simple equation. In linear form, every -equation takes the form of: - -$$ -a = ph + q -$$ - -Note the $h$ rather than $\phi$, we are formulating from Ribasim's -perspective! We can sum all coefficients for p and q to provide a linear -groundwater response to Ribasim. - -### Drainage - -From Ribasim's perspective, the groundwater head is constant given a timestep, -so that: - -\begin{align} -p = -C \\ -q = -C\phi -\end{align} - -When the head falls below the drainage elevation, the coefficients are 0. - -### River - -From Ribasim's perspective, infiltration is never limited when the head falls below -the bottom: - -\begin{align} -p = -C \\ -q = -Cb -\end{align} - -Otherwise, infiltration and drainage occur with the same equation as for the -drainage package: - -\begin{align} -p = -C \\ -q = -C\phi -\end{align} - - -# Assigning MODFLOW water levels - -Principally, MODFLOW deals with water levels; Ribasim deals with water volumes. -The translation from a water volume to a water level for a single boundary -condition is straightforward: - -\begin{align} -\Delta d = \frac{\Delta V}{A} \\ -h = b + d -\end{align} - -Where $d$ is water depth, $V$ is volume, $A$ is area, $h$ is water level, and -$b$ is the bed elevation. - -However, the primary complication is that where Ribasim has **one volume**, -MODFLOW has **many levels** to adjust. The sum of all these adjustments times -their respective areas should result in the basin volume change: - -$$ -\sum_{i=1}^{j=m} \sum_{j=1}^{i=n} \Delta d_{i,j} A_{i,j} = \Delta V_{basin} -$$ - -where $i$ is the index of the boundary condition and $j$ the index of the cell. - -It should be obvious that there are many ways to distribute this volume change -across the adjustment of every boundary condition of every cell. The main -question is when the basin volume grows or decreases, how should this volume -change be distributed across the basin? - -The best method to find an answer to this question is to run a hydraulic model, -extract water heights, and compute the total volume. This can then be used as a -lookup table for every cell. These runs can also be used for parametrizing the -volume-discharge lookup tables. In coupling to Ribasim, we need only find the -appropriate volume and assign the associated water level. For efficiency, this -lookup table can be discretized in a limited number of steps, and in coupling -the level will be interpolated. - -:::{.callout-note} -Great care is required when parametrizing these volume-level relationships. -As Ribasim does not know the properties of the surface water, it can perform -very limited validation of the volume-level lookup tables. As the total -volume of the basin is distributed across **all** boundary conditions, it -should be checked that the change of the water column for every boundary -condition matches the total volume change of the basin. -::: - -In principle, all (stationary!) hydraulic behavior of the basin can be described -approximately by these lookup tables. - -## Parametrization - -In coupling Ribasim to MODFLOW 6, relations translating the Ribasim volume must be -given **for every every cell** of every boundary condition. These consist of -piecewise linear relationships between the basin volume and its associated -water level for the boundary condition in the cell. - -These values are stored in a netCDF dataset. This dataset must meet the following -requirements: - -1. It must contain a `x` and `y` coordinate. The extent and cell size of these -coordinates must match the domain of the coupled MODFLOW 6 model exactly. -2. It must contain a variable (x, y) denoting the basin IDs. -3. It must contain a volume-level variable (x, y, row, column) for every -coupled MODFLOW 6 boundary condition, describing the volume-level lookup table -per cell. - -:::{.callout-note} -The `x` and `y` coordinates are valid for structured MODFLOW 6 models (DIS). -Discretized-by-vertices (DISV) and fully unstructured discretization (DISU). -are not yet supported, but require no fundamental changes: one basin is -connected to multiple MODFLOW 6 cells, and the coupling parameters must match -the (structured, unstructured) grid of the MODFLOW 6 model exactly. -::: - -The MODFLOW 6 coupling example cases show examples of such a parametrization. From ed8f0b8b92fdde92f01ab03f02b7c7c0630388e0 Mon Sep 17 00:00:00 2001 From: Martijn Visser Date: Tue, 16 Jan 2024 15:47:52 +0100 Subject: [PATCH 12/82] Add pixi task to update registry (#962) With our current workflow, it can happen that dev A updates the packages in Manifest.toml, and dev B gets the error: ``` ERROR: Unsatisfiable requirements detected for package X ``` The problem is that dev B's local registry is outdated, so it is not aware of the new versions of X that are being used. This adds a task to update the registry, and runs it by default when building or installing. That should make this error more rare, and perhaps easier to resolve. Note that this is an issue that may get resolved in Pkg in the future; https://github.com/JuliaLang/Pkg.jl/issues/3713 --- pixi.toml | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/pixi.toml b/pixi.toml index f3cea5339..c042758da 100644 --- a/pixi.toml +++ b/pixi.toml @@ -21,16 +21,22 @@ install-ribasim-testmodels = "pip install --no-deps --editable python/ribasim_te install-pre-commit = "pre-commit install" install-without-pre-commit = { depends_on = [ "install-julia", + "update-registry-julia", "install-ribasim-python", "install-ribasim-api", "install-ribasim-testmodels", ] } install = { depends_on = ["install-without-pre-commit", "install-pre-commit"] } # Instantiate +update-registry-julia = "julia --eval='using Pkg; Registry.update()'" instantiate-julia = "julia --project --eval='using Pkg; Pkg.instantiate()'" +initialize-julia = { depends_on = [ + "update-registry-julia", + "instantiate-julia", +] } # Docs build-julia-docs = { cmd = "julia --project=docs docs/make.jl", depends_on = [ - "instantiate-julia", + "initialize-julia", ] } quartodoc-build = { cmd = "quartodoc build && rm objects.json", cwd = "docs" } quarto-preview = { cmd = "quarto preview docs", depends_on = [ @@ -56,15 +62,15 @@ lint = { depends_on = [ # Build build-ribasim-cli = { cmd = "julia --project build.jl --app", cwd = "build/create_binaries", depends_on = [ "generate-testmodels", - "instantiate-julia", + "initialize-julia", ] } build-libribasim = { cmd = "julia --project build.jl --lib", cwd = "build/create_binaries", depends_on = [ "generate-testmodels", - "instantiate-julia", + "initialize-julia", ] } build = { "cmd" = "julia --project build.jl --app --lib", cwd = "build/create_binaries", depends_on = [ "generate-testmodels", - "instantiate-julia", + "initialize-julia", ] } remove-artifacts = "julia --eval 'rm(joinpath(Base.DEPOT_PATH[1], \"artifacts\"), force=true, recursive=true)'" From 76f4b32c651f518afe750a6960e1c418a8a1a09b Mon Sep 17 00:00:00 2001 From: Bart de Koning <74617371+SouthEndMusic@users.noreply.github.com> Date: Wed, 17 Jan 2024 13:38:06 +0100 Subject: [PATCH 13/82] Fix looped subnetwork (#965) Fixes https://github.com/Deltares/Ribasim/issues/692. It now also runs fine with the cli (which I think I ran for the first time ever ^^). --- .../ribasim_testmodels/__init__.py | 6 ++---- .../ribasim_testmodels/allocation.py | 19 +++++++++++++------ 2 files changed, 15 insertions(+), 10 deletions(-) diff --git a/python/ribasim_testmodels/ribasim_testmodels/__init__.py b/python/ribasim_testmodels/ribasim_testmodels/__init__.py index a26ee232f..0ddc0cfb1 100644 --- a/python/ribasim_testmodels/ribasim_testmodels/__init__.py +++ b/python/ribasim_testmodels/ribasim_testmodels/__init__.py @@ -7,8 +7,8 @@ import ribasim_testmodels from ribasim_testmodels.allocation import ( allocation_example_model, - # looped_subnetwork_model, fractional_flow_subnetwork_model, + looped_subnetwork_model, minimal_subnetwork_model, subnetwork_model, user_model, @@ -82,9 +82,7 @@ "subnetwork_model", "minimal_subnetwork_model", "fractional_flow_subnetwork_model", - # Disable until this issue is resolved: - # https://github.com/Deltares/Ribasim/issues/692 - # "looped_subnetwork_model", + "looped_subnetwork_model", ] # provide a mapping from model name to its constructor, so we can iterate over all models diff --git a/python/ribasim_testmodels/ribasim_testmodels/allocation.py b/python/ribasim_testmodels/ribasim_testmodels/allocation.py index c3416c4d4..4a218bd98 100644 --- a/python/ribasim_testmodels/ribasim_testmodels/allocation.py +++ b/python/ribasim_testmodels/ribasim_testmodels/allocation.py @@ -422,12 +422,15 @@ def looped_subnetwork_model(): dtype=np.int64, ) lines = node.geometry_from_connectivity(from_id, to_id) + allocation_network_id = len(from_id) * [None] + allocation_network_id[0] = 1 edge = ribasim.Edge( df=gpd.GeoDataFrame( data={ "from_node_id": from_id, "to_node_id": to_id, "edge_type": len(from_id) * ["flow"], + "allocation_network_id": allocation_network_id, }, geometry=lines, crs="EPSG:28992", @@ -454,13 +457,13 @@ def looped_subnetwork_model(): } ) - state = pd.DataFrame(data={"node_id": [2, 7, 9, 15, 17, 21], "level": 1.0}) + state = pd.DataFrame(data={"node_id": [2, 7, 9, 11, 15, 17, 21], "level": 1.0}) basin = ribasim.Basin(profile=profile, static=static, state=state) # Setup the flow boundary: flow_boundary = ribasim.FlowBoundary( - static=pd.DataFrame(data={"node_id": [5], "flow_rate": [4.5]}) + static=pd.DataFrame(data={"node_id": [5], "flow_rate": [4.5e-3]}) ) # Setup the users: @@ -468,7 +471,7 @@ def looped_subnetwork_model(): static=pd.DataFrame( data={ "node_id": [1, 12, 18, 20, 24], - "demand": 1.0, + "demand": 1.0e-3, "return_factor": 0.9, "min_level": 0.9, "priority": [2, 1, 3, 3, 2], @@ -481,8 +484,8 @@ def looped_subnetwork_model(): static=pd.DataFrame( data={ "node_id": [6, 16], - "flow_rate": 4.0, - "max_flow_rate": 4.0, + "flow_rate": 4.0e-3, + "max_flow_rate": 4.0e-3, } ) ) @@ -490,7 +493,7 @@ def looped_subnetwork_model(): # Setup the outlets: outlet = ribasim.Outlet( static=pd.DataFrame( - data={"node_id": [3, 8, 10, 22], "flow_rate": 3.0, "max_flow_rate": 3.0} + data={"node_id": [3, 8, 10, 22], "flow_rate": 3.0e-3, "max_flow_rate": 3.0} ) ) @@ -514,6 +517,9 @@ def looped_subnetwork_model(): ) ) + # Setup allocation: + allocation = ribasim.Allocation(use_allocation=True, timestep=86400) + model = ribasim.Model( network=ribasim.Network(node=node, edge=edge), basin=basin, @@ -523,6 +529,7 @@ def looped_subnetwork_model(): outlet=outlet, tabulated_rating_curve=rating_curve, terminal=terminal, + allocation=allocation, starttime="2020-01-01 00:00:00", endtime="2021-01-01 00:00:00", ) From c49adb123a43c536c1180cff9a0dec139c88bdff Mon Sep 17 00:00:00 2001 From: "git@evetion.nl" Date: Thu, 18 Jan 2024 15:54:55 +0100 Subject: [PATCH 14/82] TeamCity change in 'Ribasim' project: commit current project settings --- .../buildTypes/Ribasim_GenerateTestmodels.xml | 72 +++++++++++++++++++ .../Ribasim_Ribasim_MakeGitHubRelease.xml | 52 +++++++++++--- .../Ribasim/vcsRoots/Ribasim_Ribasim.xml | 8 +-- .../Ribasim_Linux_BuildRibasimCli.xml | 2 +- .../Ribasim_Linux_TestRibasimCli.xml | 2 +- .teamcity/Ribasim_Linux/project-config.xml | 10 --- .../Ribasim_Windows_BuildRibasimCli.xml | 2 +- .../Ribasim_Windows_TestRibasimCli.xml | 2 +- .teamcity/Ribasim_Windows/project-config.xml | 10 --- 9 files changed, 123 insertions(+), 37 deletions(-) create mode 100644 .teamcity/Ribasim/buildTypes/Ribasim_GenerateTestmodels.xml diff --git a/.teamcity/Ribasim/buildTypes/Ribasim_GenerateTestmodels.xml b/.teamcity/Ribasim/buildTypes/Ribasim_GenerateTestmodels.xml new file mode 100644 index 000000000..0b356de7c --- /dev/null +++ b/.teamcity/Ribasim/buildTypes/Ribasim_GenerateTestmodels.xml @@ -0,0 +1,72 @@ + + + Generate Testmodels + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_MakeGitHubRelease.xml b/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_MakeGitHubRelease.xml index 9796de878..e9b85c898 100644 --- a/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_MakeGitHubRelease.xml +++ b/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_MakeGitHubRelease.xml @@ -26,7 +26,8 @@ if [ -n "$tag_name" ]; then --generate-notes \ ribasim_cli_linux.zip \ ribasim_cli_windows.zip \ - ribasim_qgis.zip + ribasim_qgis.zip \ + generated_testmodels.zip echo "Release created successfully." @@ -54,12 +55,6 @@ fi]]> - - - - - - @@ -73,17 +68,21 @@ fi]]> + + + + - + - + @@ -99,6 +98,34 @@ fi]]> diff --git a/.teamcity/Ribasim/vcsRoots/Ribasim_Ribasim.xml b/.teamcity/Ribasim/vcsRoots/Ribasim_Ribasim.xml index 009f56270..6d2362381 100644 --- a/.teamcity/Ribasim/vcsRoots/Ribasim_Ribasim.xml +++ b/.teamcity/Ribasim/vcsRoots/Ribasim_Ribasim.xml @@ -3,18 +3,18 @@ Ribasim - + - - + + - + diff --git a/.teamcity/Ribasim_Linux/buildTypes/Ribasim_Linux_BuildRibasimCli.xml b/.teamcity/Ribasim_Linux/buildTypes/Ribasim_Linux_BuildRibasimCli.xml index fe7e58cb1..2e30ad363 100644 --- a/.teamcity/Ribasim_Linux/buildTypes/Ribasim_Linux_BuildRibasimCli.xml +++ b/.teamcity/Ribasim_Linux/buildTypes/Ribasim_Linux_BuildRibasimCli.xml @@ -4,7 +4,7 @@ - diff --git a/.teamcity/Ribasim_Linux/buildTypes/Ribasim_Linux_TestRibasimCli.xml b/.teamcity/Ribasim_Linux/buildTypes/Ribasim_Linux_TestRibasimCli.xml index 1567ef194..2fd093858 100644 --- a/.teamcity/Ribasim_Linux/buildTypes/Ribasim_Linux_TestRibasimCli.xml +++ b/.teamcity/Ribasim_Linux/buildTypes/Ribasim_Linux_TestRibasimCli.xml @@ -77,7 +77,7 @@ pixi run test-ribasim-cli]]> - + diff --git a/.teamcity/Ribasim_Linux/project-config.xml b/.teamcity/Ribasim_Linux/project-config.xml index 8e0b37808..5890cd0f7 100644 --- a/.teamcity/Ribasim_Linux/project-config.xml +++ b/.teamcity/Ribasim_Linux/project-config.xml @@ -3,16 +3,6 @@ Linux - - - - - - - - - - diff --git a/.teamcity/Ribasim_Windows/buildTypes/Ribasim_Windows_BuildRibasimCli.xml b/.teamcity/Ribasim_Windows/buildTypes/Ribasim_Windows_BuildRibasimCli.xml index 4c453c733..53a99c7db 100644 --- a/.teamcity/Ribasim_Windows/buildTypes/Ribasim_Windows_BuildRibasimCli.xml +++ b/.teamcity/Ribasim_Windows/buildTypes/Ribasim_Windows_BuildRibasimCli.xml @@ -4,7 +4,7 @@ - diff --git a/.teamcity/Ribasim_Windows/buildTypes/Ribasim_Windows_TestRibasimCli.xml b/.teamcity/Ribasim_Windows/buildTypes/Ribasim_Windows_TestRibasimCli.xml index 2cb6b90bd..67dd0f46f 100644 --- a/.teamcity/Ribasim_Windows/buildTypes/Ribasim_Windows_TestRibasimCli.xml +++ b/.teamcity/Ribasim_Windows/buildTypes/Ribasim_Windows_TestRibasimCli.xml @@ -66,7 +66,7 @@ - + diff --git a/.teamcity/Ribasim_Windows/project-config.xml b/.teamcity/Ribasim_Windows/project-config.xml index 7c87b36dd..44f897fe2 100644 --- a/.teamcity/Ribasim_Windows/project-config.xml +++ b/.teamcity/Ribasim_Windows/project-config.xml @@ -17,16 +17,6 @@ - - - - - - - - - - From feb0901bae5cbb5408a93717cef20cfac53b1cae Mon Sep 17 00:00:00 2001 From: Maarten Pronk Date: Thu, 18 Jan 2024 16:55:54 +0100 Subject: [PATCH 15/82] Move AWS connection to top. --- .teamcity/Ribasim/project-config.xml | 14 ++++++++++++++ .teamcity/Ribasim_Linux/project-config.xml | 14 -------------- .teamcity/Ribasim_Windows/project-config.xml | 14 -------------- 3 files changed, 14 insertions(+), 28 deletions(-) diff --git a/.teamcity/Ribasim/project-config.xml b/.teamcity/Ribasim/project-config.xml index abc9950e4..48a3307fa 100644 --- a/.teamcity/Ribasim/project-config.xml +++ b/.teamcity/Ribasim/project-config.xml @@ -46,6 +46,20 @@ + + + + + + + + + + + + + + diff --git a/.teamcity/Ribasim_Linux/project-config.xml b/.teamcity/Ribasim_Linux/project-config.xml index 5890cd0f7..2cad6ccfb 100644 --- a/.teamcity/Ribasim_Linux/project-config.xml +++ b/.teamcity/Ribasim_Linux/project-config.xml @@ -3,20 +3,6 @@ Linux - - - - - - - - - - - - - - diff --git a/.teamcity/Ribasim_Windows/project-config.xml b/.teamcity/Ribasim_Windows/project-config.xml index 44f897fe2..79e9fcbe0 100644 --- a/.teamcity/Ribasim_Windows/project-config.xml +++ b/.teamcity/Ribasim_Windows/project-config.xml @@ -3,20 +3,6 @@ Windows - - - - - - - - - - - - - - From 52bbca4319f3a88d0a64c7d1400d9210dbac838c Mon Sep 17 00:00:00 2001 From: "git@evetion.nl" Date: Thu, 18 Jan 2024 16:57:59 +0100 Subject: [PATCH 16/82] TeamCity change in 'Ribasim' project: artifact dependencies of 'Push successful nightly build to S3' build configuration were updated --- .../Ribasim_Ribasim_PushSuccessfulNightlyBuildToS3.xml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_PushSuccessfulNightlyBuildToS3.xml b/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_PushSuccessfulNightlyBuildToS3.xml index 2839b9d94..fd685aa04 100644 --- a/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_PushSuccessfulNightlyBuildToS3.xml +++ b/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_PushSuccessfulNightlyBuildToS3.xml @@ -45,14 +45,14 @@ aws s3 cp ribasim*.whl s3://ribasim/teamcity/Ribasim_Ribasim/BuildRibasimCliWind - - - - + + + + From a0b8d08842f24fc2547b9e5ffc33ab150831d684 Mon Sep 17 00:00:00 2001 From: "git@evetion.nl" Date: Thu, 18 Jan 2024 16:58:39 +0100 Subject: [PATCH 17/82] TeamCity change in 'Ribasim' project: artifact dependencies of 'Push successful nightly build to S3' build configuration were updated --- .../Ribasim_Ribasim_PushSuccessfulNightlyBuildToS3.xml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_PushSuccessfulNightlyBuildToS3.xml b/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_PushSuccessfulNightlyBuildToS3.xml index fd685aa04..3000e2534 100644 --- a/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_PushSuccessfulNightlyBuildToS3.xml +++ b/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_PushSuccessfulNightlyBuildToS3.xml @@ -49,6 +49,10 @@ aws s3 cp ribasim*.whl s3://ribasim/teamcity/Ribasim_Ribasim/BuildRibasimCliWind + + + + From 4d226ddb32f42e953a35fa1cbf27e72f9dcf102a Mon Sep 17 00:00:00 2001 From: "git@evetion.nl" Date: Thu, 18 Jan 2024 17:00:36 +0100 Subject: [PATCH 18/82] TeamCity change in 'Ribasim' project: runners of 'Push successful nightly build to S3' build configuration were updated --- .../Ribasim_Ribasim_PushSuccessfulNightlyBuildToS3.xml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_PushSuccessfulNightlyBuildToS3.xml b/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_PushSuccessfulNightlyBuildToS3.xml index 3000e2534..9fe85659d 100644 --- a/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_PushSuccessfulNightlyBuildToS3.xml +++ b/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_PushSuccessfulNightlyBuildToS3.xml @@ -11,7 +11,8 @@ set -euxo pipefail . /usr/share/Modules/init/bash module load aws -aws s3 cp ribasim_cli.zip s3://ribasim/teamcity/Ribasim_Ribasim/BuildRibasimCliWindows/latest/ribasim_cli.zip +aws s3 cp ribasim_cli_windows.zip s3://ribasim/teamcity/Ribasim_Ribasim/BuildRibasimCliWindows/latest/ribasim_cli_windows.zip +aws s3 cp ribasim_cli_linux.zip s3://ribasim/teamcity/Ribasim_Ribasim/BuildRibasimCliWindows/latest/ribasim_cli_linux.zip aws s3 cp ribasim_qgis.zip s3://ribasim/teamcity/Ribasim_Ribasim/BuildRibasimCliWindows/latest/ribasim_qgis.zip aws s3 cp ribasim*.whl s3://ribasim/teamcity/Ribasim_Ribasim/BuildRibasimCliWindows/latest/]]> From 605e5b9b20eea77cd29ab3f39f06f7bfe6933571 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 22 Jan 2024 07:48:07 +0100 Subject: [PATCH 19/82] Bump prefix-dev/setup-pixi from 0.4.1 to 0.4.3 (#974) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Bumps [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) from 0.4.1 to 0.4.3.
Release notes

Sourced from prefix-dev/setup-pixi's releases.

v0.4.3

What's Changed

🐛 Bug fixes

Full Changelog: https://github.com/prefix-dev/setup-pixi/compare/v0.4.2...v0.4.3

v0.4.2

What's Changed

✨ New features

👷🏻 CI

📝 Documentation

⬆️ Dependency updates

🤷🏻 Other changes

New Contributors

Full Changelog: https://github.com/prefix-dev/setup-pixi/compare/v0.4.1...v0.4.2

Commits

[![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=prefix-dev/setup-pixi&package-manager=github_actions&previous-version=0.4.1&new-version=0.4.3)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) ---
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/core_tests.yml | 2 +- .github/workflows/docs.yml | 2 +- .github/workflows/python_lint.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/core_tests.yml b/.github/workflows/core_tests.yml index db295c482..a5020269f 100644 --- a/.github/workflows/core_tests.yml +++ b/.github/workflows/core_tests.yml @@ -33,7 +33,7 @@ jobs: with: cache-compiled: "true" cache-registries: "true" - - uses: prefix-dev/setup-pixi@v0.4.1 + - uses: prefix-dev/setup-pixi@v0.4.3 with: pixi-version: "latest" - name: Prepare pixi diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index ccfc83f5b..ef6eea4c1 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -24,7 +24,7 @@ jobs: with: cache-compiled: "true" cache-registries: "true" - - uses: prefix-dev/setup-pixi@v0.4.1 + - uses: prefix-dev/setup-pixi@v0.4.3 with: pixi-version: "latest" - name: Prepare pixi diff --git a/.github/workflows/python_lint.yml b/.github/workflows/python_lint.yml index 12e87fafb..47310710d 100644 --- a/.github/workflows/python_lint.yml +++ b/.github/workflows/python_lint.yml @@ -16,7 +16,7 @@ jobs: continue-on-error: true steps: - uses: actions/checkout@v4 - - uses: prefix-dev/setup-pixi@v0.4.1 + - uses: prefix-dev/setup-pixi@v0.4.3 with: pixi-version: "latest" - name: Prepare pixi From dba2f9e0af735fade9e2160c33bdff98ddc7a946 Mon Sep 17 00:00:00 2001 From: Hofer-Julian <30049909+Hofer-Julian@users.noreply.github.com> Date: Mon, 22 Jan 2024 11:28:41 +0100 Subject: [PATCH 20/82] Pin number of processes used in Python tests to 4 (#975) Otherwise, some machines get stack overflow errors when running Python tests --- pixi.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.toml b/pixi.toml index c042758da..3a3fd6447 100644 --- a/pixi.toml +++ b/pixi.toml @@ -75,9 +75,9 @@ build = { "cmd" = "julia --project build.jl --app --lib", cwd = "build/create_bi remove-artifacts = "julia --eval 'rm(joinpath(Base.DEPOT_PATH[1], \"artifacts\"), force=true, recursive=true)'" # Test -test-ribasim-python = "pytest --numprocesses=auto python/ribasim/tests" +test-ribasim-python = "pytest --numprocesses=4 python/ribasim/tests" test-ribasim-api = "pytest --basetemp=python/ribasim_api/tests/temp --junitxml=report.xml python/ribasim_api/tests" -test-ribasim-cli = "pytest --numprocesses=auto --basetemp=build/ribasim_cli/tests/temp --junitxml=report.xml build/ribasim_cli/tests" +test-ribasim-cli = "pytest --numprocesses=4 --basetemp=build/ribasim_cli/tests/temp --junitxml=report.xml build/ribasim_cli/tests" test-ribasim-core = { cmd = "julia --project=core --eval 'using Pkg; Pkg.test()'", depends_on = [ "generate-testmodels", ] } From 4430e6d8e3d854f66ed519f8deee458ed517cdcb Mon Sep 17 00:00:00 2001 From: Hofer-Julian <30049909+Hofer-Julian@users.noreply.github.com> Date: Mon, 22 Jan 2024 12:36:36 +0100 Subject: [PATCH 21/82] Disable qgis tests (#976) They are red for far too long now --- .github/workflows/qgis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/qgis.yml b/.github/workflows/qgis.yml index e2dc1f0ab..67f159a35 100644 --- a/.github/workflows/qgis.yml +++ b/.github/workflows/qgis.yml @@ -11,6 +11,7 @@ jobs: test-qgis: name: "Test" runs-on: ubuntu-latest + if: false # Disable tests until we have time to fix them defaults: run: working-directory: .docker From b00b314834e567bd9c9aa037e6b06de7823600e9 Mon Sep 17 00:00:00 2001 From: hofer_jn Date: Tue, 23 Jan 2024 10:05:11 +0100 Subject: [PATCH 22/82] TeamCity change in 'Ribasim / Linux' project: build features of 'Build ribasim_cli' build configuration were updated --- .../buildTypes/Ribasim_Linux_BuildRibasimCli.xml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/.teamcity/Ribasim_Linux/buildTypes/Ribasim_Linux_BuildRibasimCli.xml b/.teamcity/Ribasim_Linux/buildTypes/Ribasim_Linux_BuildRibasimCli.xml index 2e30ad363..f203da184 100644 --- a/.teamcity/Ribasim_Linux/buildTypes/Ribasim_Linux_BuildRibasimCli.xml +++ b/.teamcity/Ribasim_Linux/buildTypes/Ribasim_Linux_BuildRibasimCli.xml @@ -90,12 +90,6 @@ pixi run build-ribasim-cli]]> - - - - - - From 9f6eb8c145f0fe3e71a9db8ec0aceb38ef69bf6a Mon Sep 17 00:00:00 2001 From: hofer_jn Date: Tue, 23 Jan 2024 10:05:56 +0100 Subject: [PATCH 23/82] TeamCity change in 'Ribasim / Linux' project: triggers of 'Test ribasim_api' build configuration were updated --- .../Ribasim_Linux/buildTypes/Ribasim_Linux_TestRibasimApi.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.teamcity/Ribasim_Linux/buildTypes/Ribasim_Linux_TestRibasimApi.xml b/.teamcity/Ribasim_Linux/buildTypes/Ribasim_Linux_TestRibasimApi.xml index 7849428d2..8fb65f23d 100644 --- a/.teamcity/Ribasim_Linux/buildTypes/Ribasim_Linux_TestRibasimApi.xml +++ b/.teamcity/Ribasim_Linux/buildTypes/Ribasim_Linux_TestRibasimApi.xml @@ -53,7 +53,7 @@ pixi run test-ribasim-api]]> - + From 839c0e69af7865a34edb4d033b4a1b5ed5438cd7 Mon Sep 17 00:00:00 2001 From: hofer_jn Date: Tue, 23 Jan 2024 10:06:26 +0100 Subject: [PATCH 24/82] TeamCity change in 'Ribasim / Linux' project: triggers of 'Test ribasim_api' build configuration were updated --- .../Ribasim_Linux/buildTypes/Ribasim_Linux_TestRibasimApi.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.teamcity/Ribasim_Linux/buildTypes/Ribasim_Linux_TestRibasimApi.xml b/.teamcity/Ribasim_Linux/buildTypes/Ribasim_Linux_TestRibasimApi.xml index 8fb65f23d..8ba314363 100644 --- a/.teamcity/Ribasim_Linux/buildTypes/Ribasim_Linux_TestRibasimApi.xml +++ b/.teamcity/Ribasim_Linux/buildTypes/Ribasim_Linux_TestRibasimApi.xml @@ -53,7 +53,7 @@ pixi run test-ribasim-api]]> - + From eb7f512d003bdc4810c9503bce18423d151aab65 Mon Sep 17 00:00:00 2001 From: Maarten Pronk <8655030+evetion@users.noreply.github.com> Date: Tue, 23 Jan 2024 10:07:52 +0100 Subject: [PATCH 25/82] Refactor `sort_keys` implementation (#970) Fixes #956 While ideally we set the sort_keys on the Schema of a TableModel, or on the TableModel themselves, this is not directly possible AFAIK: - Schemas are autogenerated, and sort_keys is not something we can serialize or parse in a JSONSchema - The TableModels are generic (TableModel[T]), so specific sort_keys can't be hardcoded to a class. The previous approach was to hold the sort keys in a `Dict[table, sort_keys]` on a NodeModel (which holds multiple tables), and passing them on when save/sort was called from the Node. This PR improves on that approach by introducing a private _sort_keys on the TableModel, which is always set (from an empty list by default) on initialization from the NodeModel. Instead of keeping a separate Dict with sort_keys on a NodeModel, we now set them in the `Field` attribute `json_schema_extra` (the only customizable attribute of a Field) for each field. Each field of a NodeModel is now validated by default (also on assignment), and if a sort_keys is present for a fieldtype, it is set on the TableModel. Based on the initial exploration by @deltamarnix in https://github.com/Deltares/Ribasim/tree/feat/sort-keys-in-tablemodel --- python/ribasim/ribasim/config.py | 122 +++++++++++---------------- python/ribasim/ribasim/input_base.py | 31 +++++-- python/ribasim/tests/test_io.py | 10 ++- 3 files changed, 79 insertions(+), 84 deletions(-) diff --git a/python/ribasim/ribasim/config.py b/python/ribasim/ribasim/config.py index e992e811b..167f8fb64 100644 --- a/python/ribasim/ribasim/config.py +++ b/python/ribasim/ribasim/config.py @@ -79,154 +79,132 @@ class Logging(ChildModel): class Terminal(NodeModel): static: TableModel[TerminalStaticSchema] = Field( - default_factory=TableModel[TerminalStaticSchema] + default_factory=TableModel[TerminalStaticSchema], + json_schema_extra={"sort_keys": ["node_id"]}, ) - _sort_keys: dict[str, list[str]] = {"static": ["node_id"]} - class PidControl(NodeModel): static: TableModel[PidControlStaticSchema] = Field( - default_factory=TableModel[PidControlStaticSchema] + default_factory=TableModel[PidControlStaticSchema], + json_schema_extra={"sort_keys": ["node_id", "control_state"]}, ) time: TableModel[PidControlTimeSchema] = Field( - default_factory=TableModel[PidControlTimeSchema] + default_factory=TableModel[PidControlTimeSchema], + json_schema_extra={"sort_keys": ["node_id", "time"]}, ) - _sort_keys: dict[str, list[str]] = { - "static": ["node_id", "control_state"], - "time": ["node_id", "time"], - } - class LevelBoundary(NodeModel): static: TableModel[LevelBoundaryStaticSchema] = Field( - default_factory=TableModel[LevelBoundaryStaticSchema] + default_factory=TableModel[LevelBoundaryStaticSchema], + json_schema_extra={"sort_keys": ["node_id"]}, ) time: TableModel[LevelBoundaryTimeSchema] = Field( - default_factory=TableModel[LevelBoundaryTimeSchema] + default_factory=TableModel[LevelBoundaryTimeSchema], + json_schema_extra={"sort_keys": ["node_id", "time"]}, ) - _sort_keys: dict[str, list[str]] = { - "static": ["node_id"], - "time": ["node_id", "time"], - } - class Pump(NodeModel): static: TableModel[PumpStaticSchema] = Field( - default_factory=TableModel[PumpStaticSchema] + default_factory=TableModel[PumpStaticSchema], + json_schema_extra={"sort_keys": ["node_id", "control_state"]}, ) - _sort_keys: dict[str, list[str]] = {"static": ["node_id", "control_state"]} - class TabulatedRatingCurve(NodeModel): static: TableModel[TabulatedRatingCurveStaticSchema] = Field( - default_factory=TableModel[TabulatedRatingCurveStaticSchema] + default_factory=TableModel[TabulatedRatingCurveStaticSchema], + json_schema_extra={"sort_keys": ["node_id", "control_state", "level"]}, ) time: TableModel[TabulatedRatingCurveTimeSchema] = Field( - default_factory=TableModel[TabulatedRatingCurveTimeSchema] + default_factory=TableModel[TabulatedRatingCurveTimeSchema], + json_schema_extra={"sort_keys": ["node_id", "time", "level"]}, ) - _sort_keys: dict[str, list[str]] = { - "static": ["node_id", "control_state", "level"], - "time": ["node_id", "time", "level"], - } class User(NodeModel): static: TableModel[UserStaticSchema] = Field( - default_factory=TableModel[UserStaticSchema] + default_factory=TableModel[UserStaticSchema], + json_schema_extra={"sort_keys": ["node_id", "priority"]}, + ) + time: TableModel[UserTimeSchema] = Field( + default_factory=TableModel[UserTimeSchema], + json_schema_extra={"sort_keys": ["node_id", "priority", "time"]}, ) - time: TableModel[UserTimeSchema] = Field(default_factory=TableModel[UserTimeSchema]) - - _sort_keys: dict[str, list[str]] = { - "static": ["node_id", "priority"], - "time": ["node_id", "priority", "time"], - } class FlowBoundary(NodeModel): static: TableModel[FlowBoundaryStaticSchema] = Field( - default_factory=TableModel[FlowBoundaryStaticSchema] + default_factory=TableModel[FlowBoundaryStaticSchema], + json_schema_extra={"sort_keys": ["node_id"]}, ) time: TableModel[FlowBoundaryTimeSchema] = Field( - default_factory=TableModel[FlowBoundaryTimeSchema] + default_factory=TableModel[FlowBoundaryTimeSchema], + json_schema_extra={"sort_keys": ["node_id", "time"]}, ) - _sort_keys: dict[str, list[str]] = { - "static": ["node_id"], - "time": ["node_id", "time"], - } - class Basin(NodeModel): profile: TableModel[BasinProfileSchema] = Field( - default_factory=TableModel[BasinProfileSchema] + default_factory=TableModel[BasinProfileSchema], + json_schema_extra={"sort_keys": ["node_id", "level"]}, ) state: TableModel[BasinStateSchema] = Field( - default_factory=TableModel[BasinStateSchema] + default_factory=TableModel[BasinStateSchema], + json_schema_extra={"sort_keys": ["node_id"]}, ) static: TableModel[BasinStaticSchema] = Field( - default_factory=TableModel[BasinStaticSchema] + default_factory=TableModel[BasinStaticSchema], + json_schema_extra={"sort_keys": ["node_id"]}, ) time: TableModel[BasinTimeSchema] = Field( - default_factory=TableModel[BasinTimeSchema] + default_factory=TableModel[BasinTimeSchema], + json_schema_extra={"sort_keys": ["node_id", "time"]}, ) subgrid: TableModel[BasinSubgridSchema] = Field( - default_factory=TableModel[BasinSubgridSchema] + default_factory=TableModel[BasinSubgridSchema], + json_schema_extra={"sort_keys": ["subgrid_id", "basin_level"]}, ) - _sort_keys: dict[str, list[str]] = { - "static": ["node_id"], - "state": ["node_id"], - "profile": ["node_id", "level"], - "time": ["node_id", "time"], - "subgrid": ["subgrid_id", "basin_level"], - } - class ManningResistance(NodeModel): static: TableModel[ManningResistanceStaticSchema] = Field( - default_factory=TableModel[ManningResistanceStaticSchema] + default_factory=TableModel[ManningResistanceStaticSchema], + json_schema_extra={"sort_keys": ["node_id", "control_state"]}, ) - _sort_keys: dict[str, list[str]] = {"static": ["node_id", "control_state"]} - class DiscreteControl(NodeModel): condition: TableModel[DiscreteControlConditionSchema] = Field( - default_factory=TableModel[DiscreteControlConditionSchema] + default_factory=TableModel[DiscreteControlConditionSchema], + json_schema_extra={ + "sort_keys": ["node_id", "listen_feature_id", "variable", "greater_than"] + }, ) logic: TableModel[DiscreteControlLogicSchema] = Field( - default_factory=TableModel[DiscreteControlLogicSchema] + default_factory=TableModel[DiscreteControlLogicSchema], + json_schema_extra={"sort_keys": ["node_id", "truth_state"]}, ) - _sort_keys: dict[str, list[str]] = { - "condition": ["node_id", "listen_feature_id", "variable", "greater_than"], - "logic": ["node_id", "truth_state"], - } - class Outlet(NodeModel): static: TableModel[OutletStaticSchema] = Field( - default_factory=TableModel[OutletStaticSchema] + default_factory=TableModel[OutletStaticSchema], + json_schema_extra={"sort_keys": ["node_id", "control_state"]}, ) - _sort_keys: dict[str, list[str]] = {"static": ["node_id", "control_state"]} - class LinearResistance(NodeModel): static: TableModel[LinearResistanceStaticSchema] = Field( - default_factory=TableModel[LinearResistanceStaticSchema] + default_factory=TableModel[LinearResistanceStaticSchema], + json_schema_extra={"sort_keys": ["node_id", "control_state"]}, ) - _sort_keys: dict[str, list[str]] = {"static": ["node_id", "control_state"]} - class FractionalFlow(NodeModel): static: TableModel[FractionalFlowStaticSchema] = Field( - default_factory=TableModel[FractionalFlowStaticSchema] + default_factory=TableModel[FractionalFlowStaticSchema], + json_schema_extra={"sort_keys": ["node_id", "control_state"]}, ) - - _sort_keys: dict[str, list[str]] = {"static": ["node_id", "control_state"]} diff --git a/python/ribasim/ribasim/input_base.py b/python/ribasim/ribasim/input_base.py index 1538bfafa..17b066d01 100644 --- a/python/ribasim/ribasim/input_base.py +++ b/python/ribasim/ribasim/input_base.py @@ -9,6 +9,7 @@ Any, Generic, TypeVar, + cast, ) import geopandas as gpd @@ -20,6 +21,8 @@ ConfigDict, DirectoryPath, Field, + PrivateAttr, + ValidationInfo, field_validator, model_serializer, model_validator, @@ -158,6 +161,7 @@ def _load(cls, filepath: Path | None) -> dict[str, Any]: class TableModel(FileModel, Generic[TableT]): df: DataFrame[TableT] | None = Field(default=None, exclude=True, repr=False) + _sort_keys: list[str] = PrivateAttr(default=[]) @field_validator("df") @classmethod @@ -219,15 +223,14 @@ def _save( self, directory: DirectoryPath, input_dir: DirectoryPath, - sort_keys: list[str] = ["node_id"], ) -> None: # TODO directory could be used to save an arrow file db_path = context_file_loading.get().get("database") if self.df is not None and self.filepath is not None: - self.sort(sort_keys) + self.sort() self._write_arrow(self.filepath, directory, input_dir) elif self.df is not None and db_path is not None: - self.sort(sort_keys) + self.sort() self._write_table(db_path) def _write_table(self, temp_path: Path) -> None: @@ -289,13 +292,13 @@ def _from_arrow(cls, path: FilePath) -> pd.DataFrame: directory = context_file_loading.get().get("directory", Path(".")) return pd.read_feather(directory / path) - def sort(self, sort_keys: list[str]): + def sort(self): """Sort the table as required. Sorting is done automatically before writing the table. """ if self.df is not None: - self.df.sort_values(sort_keys, ignore_index=True, inplace=True) + self.df.sort_values(self._sort_keys, ignore_index=True, inplace=True) @classmethod def tableschema(cls) -> TableT: @@ -374,7 +377,7 @@ def _write_table(self, path: FilePath) -> None: gdf.to_file(path, layer=self.tablename(), driver="GPKG") - def sort(self, sort_keys: list[str]): + def sort(self): self.df.sort_index(inplace=True) @@ -392,8 +395,6 @@ def check_parent(self) -> "ChildModel": class NodeModel(ChildModel): """Base class to handle combining the tables for a single node type.""" - _sort_keys: dict[str, list[str]] = {} - @model_serializer(mode="wrap") def set_modeld( self, serializer: Callable[[type["NodeModel"]], dict[str, Any]] @@ -401,6 +402,19 @@ def set_modeld( content = serializer(self) return dict(filter(lambda x: x[1], content.items())) + @field_validator("*") + @classmethod + def set_sort_keys(cls, v: Any, info: ValidationInfo) -> Any: + """Set sort keys for all TableModels if present in FieldInfo.""" + if isinstance(v, (TableModel,)): + field = cls.model_fields[getattr(info, "field_name")] + extra = field.json_schema_extra + if extra is not None and isinstance(extra, dict): + # We set sort_keys ourselves as list[str] in json_schema_extra + # but mypy doesn't know. + v._sort_keys = cast(list[str], extra.get("sort_keys", [])) + return v + @classmethod def get_input_type(cls): return cls.__name__ @@ -434,7 +448,6 @@ def _save(self, directory: DirectoryPath, input_dir: DirectoryPath, **kwargs): getattr(self, field)._save( directory, input_dir, - sort_keys=self._sort_keys[field], ) def _repr_content(self) -> str: diff --git a/python/ribasim/tests/test_io.py b/python/ribasim/tests/test_io.py index b1ac52056..e86b9456b 100644 --- a/python/ribasim/tests/test_io.py +++ b/python/ribasim/tests/test_io.py @@ -111,9 +111,13 @@ def test_sort(level_setpoint_with_minmax, tmp_path): # apply a wrong sort, then call the sort method to restore order table.df.sort_values("greater_than", ascending=False, inplace=True) assert table.df.iloc[0]["greater_than"] == 15.0 - sort_keys = model.discrete_control._sort_keys["condition"] - assert sort_keys == ["node_id", "listen_feature_id", "variable", "greater_than"] - table.sort(sort_keys) + assert table._sort_keys == [ + "node_id", + "listen_feature_id", + "variable", + "greater_than", + ] + table.sort() assert table.df.iloc[0]["greater_than"] == 5.0 # re-apply wrong sort, then check if it gets sorted on write From ec7234d41462bf4a12e77f77814cd54984d4adfb Mon Sep 17 00:00:00 2001 From: Martijn Visser Date: Tue, 23 Jan 2024 10:44:14 +0100 Subject: [PATCH 26/82] Always require 'Basin / state' as an initial condition (#977) Before we put a volume of 1 m3 in if no initial condition was given. But since this will not always work well, and there is no other number that makes a good default, it is best to remove this feature and request an explicit initial condition. --- core/src/bmi.jl | 12 ++----- core/src/utils.jl | 26 +++++++++++----- core/src/validation.jl | 24 -------------- core/test/bmi_test.jl | 2 +- core/test/run_models_test.jl | 2 +- core/test/utils_test.jl | 4 +-- .../ribasim_testmodels/backwater.py | 8 +++-- .../ribasim_testmodels/basic.py | 11 +++++-- .../ribasim_testmodels/discrete_control.py | 4 ++- .../ribasim_testmodels/invalid.py | 31 ++++++++++++++++--- .../ribasim_testmodels/time.py | 9 +++++- .../ribasim_testmodels/trivial.py | 4 ++- 12 files changed, 78 insertions(+), 59 deletions(-) diff --git a/core/src/bmi.jl b/core/src/bmi.jl index d2d7f43bb..7f11ee34d 100644 --- a/core/src/bmi.jl +++ b/core/src/bmi.jl @@ -73,16 +73,8 @@ function BMI.initialize(T::Type{Model}, config::Config)::Model end @debug "Read database into memory." - storage = if isempty(state) - # default to nearly empty basins, perhaps make required input - fill(1.0, n) - else - storages, errors = get_storages_from_levels(parameters.basin, state.level) - if errors - error("Encountered errors while parsing the initial levels of basins.") - end - storages - end + storage = get_storages_from_levels(parameters.basin, state.level) + # Synchronize level with storage set_current_basin_properties!(parameters.basin, storage) diff --git a/core/src/utils.jl b/core/src/utils.jl index 5040f786c..20ff9f75c 100644 --- a/core/src/utils.jl +++ b/core/src/utils.jl @@ -374,16 +374,28 @@ function get_storage_from_level(basin::Basin, state_idx::Int, level::Float64)::F end """Compute the storages of the basins based on the water level of the basins.""" -function get_storages_from_levels( - basin::Basin, - levels::Vector, -)::Tuple{Vector{Float64}, Bool} - storages = Float64[] +function get_storages_from_levels(basin::Basin, levels::Vector)::Vector{Float64} + errors = false + state_length = length(levels) + basin_length = length(basin.level) + if state_length != basin_length + @error "Unexpected 'Basin / state' length." state_length basin_length + errors = true + end + storages = zeros(state_length) for (i, level) in enumerate(levels) - push!(storages, get_storage_from_level(basin, i, level)) + storage = get_storage_from_level(basin, i, level) + if isnan(storage) + errors = true + end + storages[i] = storage + end + if errors + error("Encountered errors while parsing the initial levels of basins.") end - return storages, any(isnan.(storages)) + + return storages end """ diff --git a/core/src/validation.jl b/core/src/validation.jl index d49dc3506..922b02fe2 100644 --- a/core/src/validation.jl +++ b/core/src/validation.jl @@ -338,30 +338,6 @@ function variable_nt(s::Any) NamedTuple{names}((getfield(s, x) for x in names)) end -function is_consistent(node, edge, state, static, profile, time) - - # Check that node ids exist - # TODO Do we need to check the reverse as well? All ids in use? - ids = node.fid - @assert edge.from_node_id ⊆ ids "Edge from_node_id not in node ids" - @assert edge.to_node_id ⊆ ids "Edge to_node_id not in node ids" - @assert state.node_id ⊆ ids "State id not in node ids" - @assert static.node_id ⊆ ids "Static id not in node ids" - @assert profile.node_id ⊆ ids "Profile id not in node ids" - @assert time.node_id ⊆ ids "Time id not in node ids" - - # Check edges for uniqueness - @assert allunique(edge, [:from_node_id, :to_node_id]) "Duplicate edge found" - - # TODO Check states - - # TODO Check statics - - # TODO Check forcings - - true -end - # functions used by sort(x; by) sort_by_fid(row) = row.fid sort_by_id(row) = row.node_id diff --git a/core/test/bmi_test.jl b/core/test/bmi_test.jl index 8c6c95dc7..39599eeac 100644 --- a/core/test/bmi_test.jl +++ b/core/test/bmi_test.jl @@ -49,7 +49,7 @@ end toml_path = normpath(@__DIR__, "../../generated_testmodels/basic/ribasim.toml") model = BMI.initialize(Ribasim.Model, toml_path) storage0 = BMI.get_value_ptr(model, "volume") - @test storage0 == ones(4) + @test storage0 ≈ ones(4) @test_throws "Unknown variable foo" BMI.get_value_ptr(model, "foo") BMI.update_until(model, 86400.0) storage = BMI.get_value_ptr(model, "volume") diff --git a/core/test/run_models_test.jl b/core/test/run_models_test.jl index 995b07032..227ec010f 100644 --- a/core/test/run_models_test.jl +++ b/core/test/run_models_test.jl @@ -73,7 +73,7 @@ @test flow.from_node_id[1:4] == [6, typemax(Int), 0, 6] @test flow.to_node_id[1:4] == [6, typemax(Int), typemax(Int), 0] - @test basin.storage[1] == 1.0 + @test basin.storage[1] ≈ 1.0 @test basin.level[1] ≈ 0.044711584 # The exporter interpolates 1:1 for three subgrid elements, but shifted by 1.0 meter. diff --git a/core/test/utils_test.jl b/core/test/utils_test.jl index ed2bc1a1e..d4263a878 100644 --- a/core/test/utils_test.jl +++ b/core/test/utils_test.jl @@ -125,9 +125,7 @@ end logger = TestLogger() with_logger(logger) do - storages, errors = Ribasim.get_storages_from_levels(basin, [-1.0]) - @test isnan(storages[1]) - @test errors + @test_throws ErrorException Ribasim.get_storages_from_levels(basin, [-1.0]) end @test length(logger.logs) == 1 diff --git a/python/ribasim_testmodels/ribasim_testmodels/backwater.py b/python/ribasim_testmodels/ribasim_testmodels/backwater.py index e9adc4f07..42e950ec9 100644 --- a/python/ribasim_testmodels/ribasim_testmodels/backwater.py +++ b/python/ribasim_testmodels/ribasim_testmodels/backwater.py @@ -52,16 +52,17 @@ def backwater_model(): ) # Rectangular profile, width of 1.0 m. + basin_ids = ids[node_type == "Basin"] profile = pd.DataFrame( data={ - "node_id": np.repeat(ids[node_type == "Basin"], 2), + "node_id": np.repeat(basin_ids, 2), "area": [20.0, 20.0] * n_basin, "level": [0.0, 1.0] * n_basin, } ) static = pd.DataFrame( data={ - "node_id": ids[node_type == "Basin"], + "node_id": basin_ids, "drainage": 0.0, "potential_evaporation": 0.0, "infiltration": 0.0, @@ -69,7 +70,8 @@ def backwater_model(): "urban_runoff": 0.0, } ) - basin = ribasim.Basin(profile=profile, static=static) + state = pd.DataFrame(data={"node_id": basin_ids, "level": 0.05}) + basin = ribasim.Basin(profile=profile, static=static, state=state) manning_resistance = ribasim.ManningResistance( static=pd.DataFrame( diff --git a/python/ribasim_testmodels/ribasim_testmodels/basic.py b/python/ribasim_testmodels/ribasim_testmodels/basic.py index 7a3982173..657314b95 100644 --- a/python/ribasim_testmodels/ribasim_testmodels/basic.py +++ b/python/ribasim_testmodels/ribasim_testmodels/basic.py @@ -36,8 +36,10 @@ def basic_model() -> ribasim.Model: ) static = static.iloc[[0, 0, 0, 0]] static["node_id"] = [1, 3, 6, 9] - - basin = ribasim.Basin(profile=profile, static=static) + state = pd.DataFrame( + data={"node_id": static["node_id"], "level": 0.04471158417652035} + ) + basin = ribasim.Basin(profile=profile, static=static, state=state) # Setup linear resistance: linear_resistance = ribasim.LinearResistance( @@ -303,8 +305,11 @@ def tabulated_rating_curve_model() -> ribasim.Model: "urban_runoff": 0.0, } ) + state = pd.DataFrame( + data={"node_id": static["node_id"], "level": 0.04471158417652035} + ) - basin = ribasim.Basin(profile=profile, static=static) + basin = ribasim.Basin(profile=profile, static=static, state=state) # Set up a rating curve node: # Discharge: lose 1% of storage volume per day at storage = 1000.0. diff --git a/python/ribasim_testmodels/ribasim_testmodels/discrete_control.py b/python/ribasim_testmodels/ribasim_testmodels/discrete_control.py index 6481214ad..e82b606a0 100644 --- a/python/ribasim_testmodels/ribasim_testmodels/discrete_control.py +++ b/python/ribasim_testmodels/ribasim_testmodels/discrete_control.py @@ -511,7 +511,9 @@ def tabulated_rating_curve_control_model() -> ribasim.Model: } ) - basin = ribasim.Basin(profile=profile, static=static) + state = pd.DataFrame(data={"node_id": [1], "level": 0.04471158417652035}) + + basin = ribasim.Basin(profile=profile, static=static, state=state) # Set up a rating curve node: # Discharge: lose 1% of storage volume per day at storage = 100.0. diff --git a/python/ribasim_testmodels/ribasim_testmodels/invalid.py b/python/ribasim_testmodels/ribasim_testmodels/invalid.py index 19cee6613..7301f7f2a 100644 --- a/python/ribasim_testmodels/ribasim_testmodels/invalid.py +++ b/python/ribasim_testmodels/ribasim_testmodels/invalid.py @@ -61,7 +61,9 @@ def invalid_qh_model(): } ) - basin = ribasim.Basin(profile=profile, static=static) + state = pd.DataFrame(data={"node_id": [3], "level": 1.4112729908597084}) + + basin = ribasim.Basin(profile=profile, static=static, state=state) rating_curve_static = pd.DataFrame( # Invalid: levels must not be repeated @@ -171,7 +173,14 @@ def invalid_fractional_flow_model(): } ) - basin = ribasim.Basin(profile=profile, static=static) + state = pd.DataFrame( + data={ + "node_id": [1, 2], + "level": 1.4112729908597084, + } + ) + + basin = ribasim.Basin(profile=profile, static=static, state=state) # Setup terminal: terminal = ribasim.Terminal(static=pd.DataFrame(data={"node_id": [5, 6]})) @@ -263,7 +272,14 @@ def invalid_discrete_control_model(): } ) - basin = ribasim.Basin(profile=profile, static=static) + state = pd.DataFrame( + data={ + "node_id": [1, 3], + "level": 1.4112729908597084, + } + ) + + basin = ribasim.Basin(profile=profile, static=static, state=state) # Setup pump: pump = ribasim.Pump( @@ -391,7 +407,14 @@ def invalid_edge_types_model(): } ) - basin = ribasim.Basin(profile=profile, static=static) + state = pd.DataFrame( + data={ + "node_id": [1, 3], + "level": 0.04471158417652035, + } + ) + + basin = ribasim.Basin(profile=profile, static=static, state=state) # Setup pump: pump = ribasim.Pump( diff --git a/python/ribasim_testmodels/ribasim_testmodels/time.py b/python/ribasim_testmodels/ribasim_testmodels/time.py index bb34dfea7..42a0bdd6a 100644 --- a/python/ribasim_testmodels/ribasim_testmodels/time.py +++ b/python/ribasim_testmodels/ribasim_testmodels/time.py @@ -66,7 +66,14 @@ def flow_boundary_time_model(): } ) - basin = ribasim.Basin(profile=profile, static=static) + state = pd.DataFrame( + data={ + "node_id": [2], + "level": 0.04471158417652035, + } + ) + + basin = ribasim.Basin(profile=profile, static=static, state=state) n_times = 100 time = pd.date_range( diff --git a/python/ribasim_testmodels/ribasim_testmodels/trivial.py b/python/ribasim_testmodels/ribasim_testmodels/trivial.py index 664b69197..99b5067cf 100644 --- a/python/ribasim_testmodels/ribasim_testmodels/trivial.py +++ b/python/ribasim_testmodels/ribasim_testmodels/trivial.py @@ -74,6 +74,8 @@ def trivial_model() -> ribasim.Model: } ) + state = pd.DataFrame(data={"node_id": [6], "level": 0.04471158417652035}) + # Create a subgrid level interpolation from one basin to three elements. Scale one to one, but: # # 22. start at -1.0 @@ -88,7 +90,7 @@ def trivial_model() -> ribasim.Model: "subgrid_level": [-1.0, 0.0, 0.0, 1.0, 1.0, 2.0], } ) - basin = ribasim.Basin(profile=profile, static=static, subgrid=subgrid) + basin = ribasim.Basin(profile=profile, static=static, state=state, subgrid=subgrid) # Set up a rating curve node: # Discharge: lose 1% of storage volume per day at storage = 1000.0. From 8032975bc157f07371d2f922c97fd416ee23e9b7 Mon Sep 17 00:00:00 2001 From: Hofer-Julian <30049909+Hofer-Julian@users.noreply.github.com> Date: Tue, 23 Jan 2024 14:07:41 +0100 Subject: [PATCH 27/82] Add cron job to auto-update pixi lock file (#978) This way there will be a PR that updates the lock file every month --- .github/workflows/core_tests.yml | 2 +- .github/workflows/docs.yml | 2 +- .github/workflows/pixi_auto_update.yml | 32 ++++++++++++++++++++++++++ .github/workflows/pre-commit_check.yml | 2 +- .github/workflows/python_lint.yml | 2 +- .github/workflows/python_tests.yml | 2 +- .github/workflows/qgis.yml | 2 +- 7 files changed, 38 insertions(+), 6 deletions(-) create mode 100644 .github/workflows/pixi_auto_update.yml diff --git a/.github/workflows/core_tests.yml b/.github/workflows/core_tests.yml index a5020269f..50015322d 100644 --- a/.github/workflows/core_tests.yml +++ b/.github/workflows/core_tests.yml @@ -1,7 +1,7 @@ name: Julia Tests on: push: - branches: [main] + branches: [main, update/pixi-lock] paths-ignore: [".teamcity/**"] tags: ["*"] pull_request: diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index ef6eea4c1..4497abdda 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -1,7 +1,7 @@ name: Docs on: push: - branches: [main] + branches: [main, update/pixi-lock] paths-ignore: [".teamcity/**"] pull_request: merge_group: diff --git a/.github/workflows/pixi_auto_update.yml b/.github/workflows/pixi_auto_update.yml new file mode 100644 index 000000000..96e7c513a --- /dev/null +++ b/.github/workflows/pixi_auto_update.yml @@ -0,0 +1,32 @@ +name: Pixi auto update + +on: + schedule: + # At 03:00 on day 1 of the month + - cron: "0 3 1 * *" + # on demand + workflow_dispatch: + +jobs: + auto-update: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + with: + ssh-key: ${{ secrets.SSH_PRIVATE_KEY }} + - uses: prefix-dev/setup-pixi@v0.4.3 + with: + pixi-version: "latest" + cache: false + - name: Update pixi lock file + run: | + rm pixi.lock + pixi install + - uses: peter-evans/create-pull-request@v5 + with: + token: ${{ secrets.GITHUB_TOKEN }} + branch: update/pixi-lock + title: Update pixi lock file + commit-message: "Update `pixi.lock`" + body: Update pixi dependencies to the latest version. + author: "GitHub " diff --git a/.github/workflows/pre-commit_check.yml b/.github/workflows/pre-commit_check.yml index 17d1ae7a2..fb5f88949 100644 --- a/.github/workflows/pre-commit_check.yml +++ b/.github/workflows/pre-commit_check.yml @@ -4,7 +4,7 @@ on: pull_request: merge_group: push: - branches: [main, update/pre-commit-hooks] + branches: [main, update/pre-commit-hooks, update/pixi-lock] jobs: check: diff --git a/.github/workflows/python_lint.yml b/.github/workflows/python_lint.yml index 47310710d..a5a08c9a5 100644 --- a/.github/workflows/python_lint.yml +++ b/.github/workflows/python_lint.yml @@ -1,7 +1,7 @@ name: Python Lint on: push: - branches: [main] + branches: [main, update/pixi-lock] paths-ignore: [".teamcity/**"] tags: ["*"] pull_request: diff --git a/.github/workflows/python_tests.yml b/.github/workflows/python_tests.yml index 07022ddde..6089785e8 100644 --- a/.github/workflows/python_tests.yml +++ b/.github/workflows/python_tests.yml @@ -1,7 +1,7 @@ name: Ribasim Python Tests on: push: - branches: [main] + branches: [main, update/pixi-lock] paths-ignore: [".teamcity/**"] tags: ["*"] pull_request: diff --git a/.github/workflows/qgis.yml b/.github/workflows/qgis.yml index 67f159a35..608820001 100644 --- a/.github/workflows/qgis.yml +++ b/.github/workflows/qgis.yml @@ -2,7 +2,7 @@ name: QGIS Tests on: push: - branches: [main] + branches: [main, update/pixi-lock] paths-ignore: [".teamcity/**"] tags: ["*"] pull_request: From 616e642bfeca9a846b57f44da099f84a0f23917f Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue, 23 Jan 2024 14:34:36 +0100 Subject: [PATCH 28/82] Update pixi lock file (#979) Update pixi dependencies to the latest version. Co-authored-by: GitHub --- pixi.lock | 3407 +++++++++++++++++++++++++++-------------------------- 1 file changed, 1707 insertions(+), 1700 deletions(-) diff --git a/pixi.lock b/pixi.lock index d9ecf8b92..ac270a7a4 100644 --- a/pixi.lock +++ b/pixi.lock @@ -2283,7 +2283,7 @@ package: - azure-core-cpp >=1.10.3,<2.0a0 - libgcc-ng >=12 - libstdcxx-ng >=12 - - libxml2 >=2.12.1,<2.13.0a0 + - libxml2 >=2.12.1,<3.0.0a0 - openssl >=3.2.0,<4.0a0 url: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-common-cpp-12.5.0-hb858b4b_2.conda hash: @@ -2306,7 +2306,7 @@ package: - __osx >=10.9 - azure-core-cpp >=1.10.3,<2.0a0 - libcxx >=16.0.6 - - libxml2 >=2.12.1,<2.13.0a0 + - libxml2 >=2.12.1,<3.0.0a0 - openssl >=3.2.0,<4.0a0 url: https://conda.anaconda.org/conda-forge/osx-64/azure-storage-common-cpp-12.5.0-hf4badfb_2.conda hash: @@ -2329,7 +2329,7 @@ package: - __osx >=10.9 - azure-core-cpp >=1.10.3,<2.0a0 - libcxx >=16.0.6 - - libxml2 >=2.12.1,<2.13.0a0 + - libxml2 >=2.12.1,<3.0.0a0 - openssl >=3.2.0,<4.0a0 url: https://conda.anaconda.org/conda-forge/osx-arm64/azure-storage-common-cpp-12.5.0-h607ffeb_2.conda hash: @@ -2535,16 +2535,16 @@ package: timestamp: 1695447533107 - 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platform: osx-64 name: xarray - version: 2023.12.0 + version: 2024.1.0 category: main manager: conda dependencies: - - numpy >=1.22 - - packaging >=21.3 - - pandas >=1.4 + - numpy >=1.23 + - packaging >=22 + - pandas >=1.5 - python >=3.9 - url: https://conda.anaconda.org/conda-forge/noarch/xarray-2023.12.0-pyhd8ed1ab_0.conda + url: https://conda.anaconda.org/conda-forge/noarch/xarray-2024.1.0-pyhd8ed1ab_0.conda hash: - md5: e9b31d3ab1b0dd5fd8c24419f6560b90 - sha256: ab89b70aa3d31a9cacf0e91a7c7a6f8cc45d866d71cdcee1219561cff0e8a9a5 + md5: 7103106672d9b25f2b2270797307698e + sha256: e314765c30225ccff7a2ddfc4d01de424b955bab595ca8b1104d02f53d53a26d build: pyhd8ed1ab_0 arch: x86_64 subdir: osx-64 build_number: 0 constrains: - - flox >=0.5 + - distributed >=2022.7 - hdf5 >=1.12 - - iris >=3.2 - h5netcdf >=1.0 - - h5py >=3.6 - - distributed >=2022.7 - - pint >=0.19 + - toolz >=0.12 - nc-time-axis >=1.4 - - scipy >=1.8 + - cartopy >=0.20 + - bottleneck >=1.3 + - pint >=0.19 - seaborn >=0.11 - - dask-core >=2022.7 - 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platform: linux-64 name: xcb-util version: 0.4.0 From 8af3073ee0d78e8c31f042214d0eeabca8dba11a Mon Sep 17 00:00:00 2001 From: Hofer-Julian <30049909+Hofer-Julian@users.noreply.github.com> Date: Tue, 23 Jan 2024 15:55:00 +0100 Subject: [PATCH 29/82] Auto update Julia manifest (#980) As discussed: https://github.com/Deltares/Ribasim/pull/978#pullrequestreview-1838741269 --- .github/workflows/core_tests.yml | 2 +- .github/workflows/docs.yml | 2 +- .github/workflows/julia_auto_update.yml | 31 +++++++++++++++++++++++++ pixi.toml | 1 + 4 files changed, 34 insertions(+), 2 deletions(-) create mode 100644 .github/workflows/julia_auto_update.yml diff --git a/.github/workflows/core_tests.yml b/.github/workflows/core_tests.yml index 50015322d..9e57902fb 100644 --- a/.github/workflows/core_tests.yml +++ b/.github/workflows/core_tests.yml @@ -1,7 +1,7 @@ name: Julia Tests on: push: - branches: [main, update/pixi-lock] + branches: [main, update/pixi-lock, update/julia-manifest] paths-ignore: [".teamcity/**"] tags: ["*"] pull_request: diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 4497abdda..0bba37774 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -1,7 +1,7 @@ name: Docs on: push: - branches: [main, update/pixi-lock] + branches: [main, update/pixi-lock, update/julia-manifest] paths-ignore: [".teamcity/**"] pull_request: merge_group: diff --git a/.github/workflows/julia_auto_update.yml b/.github/workflows/julia_auto_update.yml new file mode 100644 index 000000000..42de6be7e --- /dev/null +++ b/.github/workflows/julia_auto_update.yml @@ -0,0 +1,31 @@ +name: Julia auto update + +on: + schedule: + # At 03:00 on day 1 of the month + - cron: "0 3 1 * *" + # on demand + workflow_dispatch: + +jobs: + auto-update: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + with: + ssh-key: ${{ secrets.SSH_PRIVATE_KEY }} + - uses: prefix-dev/setup-pixi@v0.4.3 + with: + pixi-version: "latest" + - name: Update pixi lock file + run: | + pixi run update-manifest-julia + pixi install + - uses: peter-evans/create-pull-request@v5 + with: + token: ${{ secrets.GITHUB_TOKEN }} + branch: update/julia-manifest + title: Update Julia manifest + commit-message: "Update Julia manifest" + body: Update Julia dependencies to the latest version. + author: "GitHub " diff --git a/pixi.toml b/pixi.toml index 3a3fd6447..27342235e 100644 --- a/pixi.toml +++ b/pixi.toml @@ -29,6 +29,7 @@ install-without-pre-commit = { depends_on = [ install = { depends_on = ["install-without-pre-commit", "install-pre-commit"] } # Instantiate update-registry-julia = "julia --eval='using Pkg; Registry.update()'" +update-manifest-julia = "julia --eval='using Pkg; Pkg.update()'" instantiate-julia = "julia --project --eval='using Pkg; Pkg.instantiate()'" initialize-julia = { depends_on = [ "update-registry-julia", From 9e0435353540f4fb1891b79ad5aec81b8d18a156 Mon Sep 17 00:00:00 2001 From: Hofer-Julian Date: Tue, 23 Jan 2024 16:12:26 +0100 Subject: [PATCH 30/82] Fix copy paste mistake --- .github/workflows/julia_auto_update.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/julia_auto_update.yml b/.github/workflows/julia_auto_update.yml index 42de6be7e..d745eb34c 100644 --- a/.github/workflows/julia_auto_update.yml +++ b/.github/workflows/julia_auto_update.yml @@ -17,7 +17,7 @@ jobs: - uses: prefix-dev/setup-pixi@v0.4.3 with: pixi-version: "latest" - - name: Update pixi lock file + - name: Update Julia manifest file run: | pixi run update-manifest-julia pixi install From d9288704268a2a40817ee951ae43b1a9ec3ae4d0 Mon Sep 17 00:00:00 2001 From: Martijn Visser Date: Wed, 24 Jan 2024 10:01:10 +0100 Subject: [PATCH 31/82] Julia manifest update the root environment (#981) Instead to the global one. Now it works, I manually triggered the action from this branch in #982. --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: GitHub --- Manifest.toml | 80 +++++++++++++++++++++++++++------------------------ pixi.toml | 2 +- 2 files changed, 43 insertions(+), 39 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index a4e91fb27..b7c0d6488 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -138,9 +138,9 @@ version = "0.1.5" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" +git-tree-sha1 = "9e2a6b69137e6969bab0152632dcb3bc108c8bdd" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" -version = "1.0.8+0" +version = "1.0.8+1" [[deps.CPUSummary]] deps = ["CpuId", "IfElse", "PrecompileTools", "Static"] @@ -190,9 +190,9 @@ version = "0.7.3" [[deps.CodecZstd]] deps = ["TranscodingStreams", "Zstd_jll"] -git-tree-sha1 = "f69e46bf7b307d15a896b57d5b3321c01cd64923" +git-tree-sha1 = "23373fecba848397b1705f6183188a0c0bc86917" uuid = "6b39b394-51ab-5f42-8807-6242bab2b4c2" -version = "0.8.1" +version = "0.8.2" [[deps.CommonSolve]] git-tree-sha1 = "0eee5eb66b1cf62cd6ad1b460238e60e4b09400c" @@ -207,9 +207,9 @@ version = "0.3.0" [[deps.Compat]] deps = ["TOML", "UUIDs"] -git-tree-sha1 = "ed2ebb1ff7550226ddb584ba8352facf8d9ffb22" +git-tree-sha1 = "75bd5b6fc5089df449b5d35fa501c846c9b6549b" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.11.0" +version = "4.12.0" weakdeps = ["Dates", "LinearAlgebra"] [deps.Compat.extensions] @@ -309,9 +309,9 @@ uuid = "a10d1c49-ce27-4219-8d33-6db1a4562965" version = "2.5.0" [[deps.DataAPI]] -git-tree-sha1 = "8da84edb865b0b5b0100c0666a9bc9a0b71c553c" +git-tree-sha1 = "abe83f3a2f1b857aac70ef8b269080af17764bbe" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.15.0" +version = "1.16.0" [[deps.DataFrames]] deps = ["Compat", "DataAPI", "DataStructures", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrecompileTools", "PrettyTables", "Printf", "REPL", "Random", "Reexport", "SentinelArrays", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] @@ -355,15 +355,15 @@ uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" [[deps.Dictionaries]] deps = ["Indexing", "Random", "Serialization"] -git-tree-sha1 = "e82c3c97b5b4ec111f3c1b55228cebc7510525a2" +git-tree-sha1 = "5bde104a45593207307e1481a58e0339d4643fca" uuid = "85a47980-9c8c-11e8-2b9f-f7ca1fa99fb4" -version = "0.3.25" +version = "0.3.26" [[deps.DiffEqBase]] deps = ["ArrayInterface", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces"] -git-tree-sha1 = "044648af911974c3928058c1f8c83f159dece274" +git-tree-sha1 = "6af33c2eb7478db06bcf5c810e6f3dda53aac2ac" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.145.6" +version = "6.146.0" [deps.DiffEqBase.extensions] DiffEqBaseChainRulesCoreExt = "ChainRulesCore" @@ -598,9 +598,9 @@ version = "1.9.0" [[deps.HiGHS]] deps = ["HiGHS_jll", "MathOptInterface", "PrecompileTools", "SparseArrays"] -git-tree-sha1 = "fce13308f09771b160232903cad57be39a8a0ebb" +git-tree-sha1 = "2b650f670ad691b94f506e88b4f3ab591a13f809" uuid = "87dc4568-4c63-4d18-b0c0-bb2238e4078b" -version = "1.7.5" +version = "1.8.0" [[deps.HiGHS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl"] @@ -622,9 +622,9 @@ version = "1.24.2" [[deps.IOCapture]] deps = ["Logging", "Random"] -git-tree-sha1 = "d75853a0bdbfb1ac815478bacd89cd27b550ace6" +git-tree-sha1 = "8b72179abc660bfab5e28472e019392b97d0985c" uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" -version = "0.2.3" +version = "0.2.4" [[deps.IfElse]] git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" @@ -691,9 +691,9 @@ version = "1.0.0" [[deps.JLD2]] deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "PrecompileTools", "Printf", "Reexport", "Requires", "TranscodingStreams", "UUIDs"] -git-tree-sha1 = "853b9e0b876e8c7093a824c4f83c619d23525e64" +git-tree-sha1 = "7c0008f0b7622c6c0ee5c65cbc667b69f8a65672" uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819" -version = "0.4.43" +version = "0.4.45" [[deps.JLLWrappers]] deps = ["Artifacts", "Preferences"] @@ -900,9 +900,9 @@ weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] [[deps.LoweredCodeUtils]] deps = ["JuliaInterpreter"] -git-tree-sha1 = "38756922d32476c8f41f73560b910fc805a5a103" +git-tree-sha1 = "20ce1091ba18bcdae71ad9b71ee2367796ba6c48" uuid = "6f1432cf-f94c-5a45-995e-cdbf5db27b0b" -version = "2.4.3" +version = "2.4.4" [[deps.Lz4_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -918,9 +918,9 @@ version = "2024.0.0+0" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "b211c553c199c111d998ecdaf7623d1b89b69f93" +git-tree-sha1 = "2fa9ee3e63fd3a4f7a9a4f4744a52f4856de82df" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.12" +version = "0.5.13" [[deps.ManualMemory]] git-tree-sha1 = "bcaef4fc7a0cfe2cba636d84cda54b5e4e4ca3cd" @@ -1025,10 +1025,10 @@ uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" version = "1.2.0" [[deps.NonlinearSolve]] -deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "EnumX", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "LazyArrays", "LineSearches", "LinearAlgebra", "LinearSolve", "MaybeInplace", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] -git-tree-sha1 = "72b036b728461272ae1b1c3f7096cb4c319d8793" +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "LazyArrays", "LineSearches", "LinearAlgebra", "LinearSolve", "MaybeInplace", "PrecompileTools", "Preferences", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "TimerOutputs"] +git-tree-sha1 = "78bdd3a4a62865cf43c53d63783b0cbfddcdbbe6" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "3.4.0" +version = "3.5.0" [deps.NonlinearSolve.extensions] NonlinearSolveBandedMatricesExt = "BandedMatrices" @@ -1203,9 +1203,9 @@ version = "1.3.4" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "SparseArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "4943624c0e437ddf6362a82e5319bc8e83d80857" +git-tree-sha1 = "dd7fc1923fde0cc6cdff451352d17924b0704ca1" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "3.5.2" +version = "3.5.4" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" @@ -1291,9 +1291,9 @@ version = "3.43.0+0" [[deps.SciMLBase]] deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FillArrays", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] -git-tree-sha1 = "b2714ddd879525c825f427e861f5059a96b287f7" +git-tree-sha1 = "de41474ac529bf81598e064587421cc5ebc28fa0" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.18.0" +version = "2.20.0" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -1344,16 +1344,18 @@ deps = ["Distributed", "Mmap", "Random", "Serialization"] uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383" [[deps.SimpleNonlinearSolve]] -deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "MaybeInplace", "PrecompileTools", "Reexport", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "8d672bd91dc432fb286b6d4bcf1a5dc417e932a3" +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "MaybeInplace", "PrecompileTools", "Reexport", "SciMLBase", "StaticArraysCore"] +git-tree-sha1 = "470c5f97af31fa35926b45eb01e53a46c8d7d35f" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "1.2.0" +version = "1.3.1" [deps.SimpleNonlinearSolve.extensions] SimpleNonlinearSolvePolyesterForwardDiffExt = "PolyesterForwardDiff" + SimpleNonlinearSolveStaticArraysExt = "StaticArrays" [deps.SimpleNonlinearSolve.weakdeps] PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" [[deps.SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] @@ -1388,17 +1390,19 @@ version = "1.10.0" [[deps.SparseDiffTools]] deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "Tricks", "UnPack", "VertexSafeGraphs"] -git-tree-sha1 = "c281e11db4eacb36a292a054bac83c5a0aca2a26" +git-tree-sha1 = "3b38ae7a1cbe9b8b1344359599753957644b03d4" uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" -version = "2.15.0" +version = "2.16.0" [deps.SparseDiffTools.extensions] SparseDiffToolsEnzymeExt = "Enzyme" + SparseDiffToolsPolyesterForwardDiffExt = "PolyesterForwardDiff" SparseDiffToolsSymbolicsExt = "Symbolics" SparseDiffToolsZygoteExt = "Zygote" [deps.SparseDiffTools.weakdeps] Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b" Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" @@ -1437,9 +1441,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"] [[deps.StaticArrays]] deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] -git-tree-sha1 = "4e17a790909b17f7bf1496e3aec138cf01b60b3b" +git-tree-sha1 = "f68dd04d131d9a8a8eb836173ee8f105c360b0c5" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.9.0" +version = "1.9.1" weakdeps = ["ChainRulesCore", "Statistics"] [deps.StaticArrays.extensions] @@ -1476,9 +1480,9 @@ version = "0.3.4" [[deps.StructArrays]] deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] -git-tree-sha1 = "0a3db38e4cce3c54fe7a71f831cd7b6194a54213" +git-tree-sha1 = "1b0b1205a56dc288b71b1961d48e351520702e24" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.16" +version = "0.6.17" [[deps.StructTypes]] deps = ["Dates", "UUIDs"] diff --git a/pixi.toml b/pixi.toml index 27342235e..27ff761d0 100644 --- a/pixi.toml +++ b/pixi.toml @@ -29,7 +29,7 @@ install-without-pre-commit = { depends_on = [ install = { depends_on = ["install-without-pre-commit", "install-pre-commit"] } # Instantiate update-registry-julia = "julia --eval='using Pkg; Registry.update()'" -update-manifest-julia = "julia --eval='using Pkg; Pkg.update()'" +update-manifest-julia = "julia --project --eval='using Pkg; Pkg.update()'" instantiate-julia = "julia --project --eval='using Pkg; Pkg.instantiate()'" initialize-julia = { depends_on = [ "update-registry-julia", From 2d7c382476b142c10ae859bc1bca3086f15cc940 Mon Sep 17 00:00:00 2001 From: Huite Date: Thu, 25 Jan 2024 12:46:34 +0100 Subject: [PATCH 32/82] Add update_subgrid_level to BMI functions (#986) Fixes #985 --- build/libribasim/src/libribasim.jl | 6 ++++++ core/src/bmi.jl | 5 +++++ python/ribasim_api/tests/test_bmi.py | 11 +++++++++++ python/ribasim_testmodels/ribasim_testmodels/basic.py | 11 ++++++++++- 4 files changed, 32 insertions(+), 1 deletion(-) diff --git a/build/libribasim/src/libribasim.jl b/build/libribasim/src/libribasim.jl index ccaf3fb54..ee216288f 100644 --- a/build/libribasim/src/libribasim.jl +++ b/build/libribasim/src/libribasim.jl @@ -100,6 +100,12 @@ Base.@ccallable function update_until(time::Cdouble)::Cint end end +Base.@ccallable function update_subgrid_level()::Cint + @try_c begin + Ribasim.update_subgrid_level(model) + end +end + Base.@ccallable function get_current_time(time::Ptr{Cdouble})::Cint @try_c begin t = BMI.get_current_time(model) diff --git a/core/src/bmi.jl b/core/src/bmi.jl index 7f11ee34d..9b9a7993d 100644 --- a/core/src/bmi.jl +++ b/core/src/bmi.jl @@ -633,6 +633,11 @@ function BMI.update_until(model::Model, time)::Model return model end +function update_subgrid_level(model::Model)::Model + update_subgrid_level!(model.integrator) + return model +end + function BMI.get_value_ptr(model::Model, name::AbstractString) if name == "volume" model.integrator.u.storage diff --git a/python/ribasim_api/tests/test_bmi.py b/python/ribasim_api/tests/test_bmi.py index 4318eec81..01342a274 100644 --- a/python/ribasim_api/tests/test_bmi.py +++ b/python/ribasim_api/tests/test_bmi.py @@ -57,6 +57,17 @@ def test_update_until(libribasim, basic, tmp_path): assert actual_time == pytest.approx(expected_time) +def test_update_subgrid_level(libribasim, basic, tmp_path): + basic.write(tmp_path / "ribasim.toml") + config_file = str(tmp_path / "ribasim.toml") + libribasim.initialize(config_file) + libribasim.update_subgrid_level() + level = libribasim.get_value_ptr("subgrid_level") + # The subgrid levels are initialized with NaN. + # After calling update, they should have regular values. + assert np.isfinite(level).all() + + def test_get_var_type(libribasim, basic, tmp_path): basic.write(tmp_path / "ribasim.toml") config_file = str(tmp_path / "ribasim.toml") diff --git a/python/ribasim_testmodels/ribasim_testmodels/basic.py b/python/ribasim_testmodels/ribasim_testmodels/basic.py index 657314b95..8d449d8c2 100644 --- a/python/ribasim_testmodels/ribasim_testmodels/basic.py +++ b/python/ribasim_testmodels/ribasim_testmodels/basic.py @@ -39,7 +39,16 @@ def basic_model() -> ribasim.Model: state = pd.DataFrame( data={"node_id": static["node_id"], "level": 0.04471158417652035} ) - basin = ribasim.Basin(profile=profile, static=static, state=state) + # This is a 1:1 translation. + subgrid = pd.DataFrame( + data={ + "node_id": profile["node_id"], + "subgrid_id": profile["node_id"], + "basin_level": profile["level"], + "subgrid_level": profile["level"], + } + ) + basin = ribasim.Basin(profile=profile, static=static, state=state, subgrid=subgrid) # Setup linear resistance: linear_resistance = ribasim.LinearResistance( From 9763561ea51630a826df5f2fd9dad592e33f721c Mon Sep 17 00:00:00 2001 From: Martijn Visser Date: Thu, 25 Jan 2024 13:42:38 +0100 Subject: [PATCH 33/82] Pin pandas to less noisy 2.1.4 (#988) Addresses part of #984, at least for our dev environment. I'm keeping #984 open to remind us to unpin it when a new pandera is out. This also adds [xugrid](https://github.com/Deltares/xugrid) and netCDF4 to our pixi environment. Not as a ribasim dependency, but will need it to run conversion scripts from #969. --- pixi.lock | 4458 ++++++++++++++++++++++++++++++++++++++++------------- pixi.toml | 6 +- 2 files changed, 3371 insertions(+), 1093 deletions(-) diff --git a/pixi.lock b/pixi.lock index ac270a7a4..b076825ff 100644 --- a/pixi.lock +++ b/pixi.lock @@ -311,15 +311,15 @@ package: timestamp: 1649077760928 - platform: linux-64 name: argcomplete - version: 3.2.1 + version: 3.2.2 category: main manager: conda dependencies: - python >=3.8 - url: https://conda.anaconda.org/conda-forge/noarch/argcomplete-3.2.1-pyhd8ed1ab_0.conda + url: https://conda.anaconda.org/conda-forge/noarch/argcomplete-3.2.2-pyhd8ed1ab_0.conda hash: - md5: 0801250abb3d5b86010e20324f0dde94 - sha256: af221f16a23feea4d91db75b35c5720c9c448814af815fe6d45c5627eb75e897 + md5: 4017741f57d9bbf3cf184ca147859f78 + sha256: 8a1d1f92d40c6686d10ecce290a42560d023ecc02676f54dcfedfc0ede354f52 build: pyhd8ed1ab_0 arch: x86_64 subdir: linux-64 @@ -327,19 +327,19 @@ package: license: Apache-2.0 license_family: Apache noarch: python - size: 40094 - timestamp: 1702228373768 + size: 40113 + timestamp: 1706095451334 - platform: osx-64 name: argcomplete - version: 3.2.1 + version: 3.2.2 category: main manager: conda dependencies: - python >=3.8 - url: https://conda.anaconda.org/conda-forge/noarch/argcomplete-3.2.1-pyhd8ed1ab_0.conda + url: https://conda.anaconda.org/conda-forge/noarch/argcomplete-3.2.2-pyhd8ed1ab_0.conda hash: - md5: 0801250abb3d5b86010e20324f0dde94 - sha256: af221f16a23feea4d91db75b35c5720c9c448814af815fe6d45c5627eb75e897 + md5: 4017741f57d9bbf3cf184ca147859f78 + sha256: 8a1d1f92d40c6686d10ecce290a42560d023ecc02676f54dcfedfc0ede354f52 build: pyhd8ed1ab_0 arch: x86_64 subdir: osx-64 @@ -347,19 +347,19 @@ package: license: Apache-2.0 license_family: Apache noarch: python - size: 40094 - timestamp: 1702228373768 + size: 40113 + timestamp: 1706095451334 - platform: osx-arm64 name: argcomplete - version: 3.2.1 + version: 3.2.2 category: main manager: conda dependencies: - python >=3.8 - url: https://conda.anaconda.org/conda-forge/noarch/argcomplete-3.2.1-pyhd8ed1ab_0.conda + url: https://conda.anaconda.org/conda-forge/noarch/argcomplete-3.2.2-pyhd8ed1ab_0.conda hash: - 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dask + - geopandas + - numba >=0.50 + - numba_celltree + - numpy + - pandas + - pooch + - python >=3.9 + - scipy + - shapely >=2.0 + - xarray >=0.15 + url: https://conda.anaconda.org/conda-forge/noarch/xugrid-0.8.1-pyhd8ed1ab_0.conda + hash: + md5: 5771e469daca73194129ea67ec474efc + sha256: 4b7ce5952dcd4f29de009d30f8d845290a629c0bc006cb403ec9f595f53da4b6 + build: pyhd8ed1ab_0 + arch: x86_64 + subdir: win-64 + build_number: 0 + license: MIT + license_family: MIT + noarch: python + size: 91565 + timestamp: 1705930436538 - platform: linux-64 name: xyzservices version: 2023.10.1 @@ -38801,6 +40997,86 @@ package: license_family: MOZILLA size: 4210250 timestamp: 1697057168534 +- platform: linux-64 + name: zict + version: 3.0.0 + category: main + manager: conda + dependencies: + - python >=3.8 + url: https://conda.anaconda.org/conda-forge/noarch/zict-3.0.0-pyhd8ed1ab_0.conda + hash: + md5: cf30c2c15b82aacb07f9c09e28ff2275 + sha256: 3d65c081514569ab3642ba7e6c2a6b4615778b596db6b1c82ee30a2d912539e5 + build: pyhd8ed1ab_0 + arch: x86_64 + subdir: linux-64 + build_number: 0 + license: BSD-3-Clause + license_family: BSD + noarch: python + size: 36325 + timestamp: 1681770298596 +- platform: osx-64 + name: zict + version: 3.0.0 + category: main + manager: conda + dependencies: + - python >=3.8 + url: https://conda.anaconda.org/conda-forge/noarch/zict-3.0.0-pyhd8ed1ab_0.conda + hash: + md5: cf30c2c15b82aacb07f9c09e28ff2275 + sha256: 3d65c081514569ab3642ba7e6c2a6b4615778b596db6b1c82ee30a2d912539e5 + build: pyhd8ed1ab_0 + arch: x86_64 + subdir: osx-64 + build_number: 0 + license: BSD-3-Clause + license_family: BSD + noarch: python + size: 36325 + timestamp: 1681770298596 +- platform: osx-arm64 + name: zict + version: 3.0.0 + category: main + manager: conda + dependencies: + - python >=3.8 + url: https://conda.anaconda.org/conda-forge/noarch/zict-3.0.0-pyhd8ed1ab_0.conda + hash: + md5: cf30c2c15b82aacb07f9c09e28ff2275 + sha256: 3d65c081514569ab3642ba7e6c2a6b4615778b596db6b1c82ee30a2d912539e5 + build: pyhd8ed1ab_0 + arch: aarch64 + subdir: osx-arm64 + build_number: 0 + license: BSD-3-Clause + license_family: BSD + noarch: python + size: 36325 + timestamp: 1681770298596 +- platform: win-64 + name: zict + version: 3.0.0 + category: main + manager: conda + dependencies: + - python >=3.8 + url: https://conda.anaconda.org/conda-forge/noarch/zict-3.0.0-pyhd8ed1ab_0.conda + hash: + md5: cf30c2c15b82aacb07f9c09e28ff2275 + sha256: 3d65c081514569ab3642ba7e6c2a6b4615778b596db6b1c82ee30a2d912539e5 + build: pyhd8ed1ab_0 + arch: x86_64 + subdir: win-64 + build_number: 0 + license: BSD-3-Clause + license_family: BSD + noarch: python + size: 36325 + timestamp: 1681770298596 - platform: linux-64 name: zipp version: 3.17.0 diff --git a/pixi.toml b/pixi.toml index 27ff761d0..1f1d5183e 100644 --- a/pixi.toml +++ b/pixi.toml @@ -127,12 +127,14 @@ ribasim-model = "julia --project=core -e 'using Ribasim; Ribasim.main(ARGS)'" build = "*" datamodel-code-generator = "0.24.*" geopandas = "*" +hatchling = "*" juliaup = "*" jupyterlab = "*" libgdal-arrow-parquet = "*" matplotlib = "*" mypy = "*" -pandas = "*" +netCDF4 = "*" +pandas = "==2.1.4" # Avoid excessive deprecation warnings from pandera (#984) pandas-stubs = "*" pandera = "*" pip = "*" @@ -158,7 +160,7 @@ types-requests = "*" typing-extensions = ">=4.6" xarray = "*" xmipy = "*" -hatchling = "*" +xugrid = "*" [target.win-64.dependencies] quarto = "*" From 9581d7bd80407128f2fdce56acd4530a5bde7e14 Mon Sep 17 00:00:00 2001 From: Huite Date: Thu, 25 Jan 2024 17:07:32 +0100 Subject: [PATCH 34/82] Not part of bmi/xmi: add the method to python api (#990) Second chance... --- python/ribasim_api/ribasim_api/ribasim_api.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/python/ribasim_api/ribasim_api/ribasim_api.py b/python/ribasim_api/ribasim_api/ribasim_api.py index 6914deae8..341f1e7c4 100644 --- a/python/ribasim_api/ribasim_api/ribasim_api.py +++ b/python/ribasim_api/ribasim_api/ribasim_api.py @@ -27,3 +27,6 @@ def init_julia(self) -> None: def shutdown_julia(self) -> None: self.lib.shutdown_julia(c_int(0)) + + def update_subgrid_level(self) -> None: + self.lib.update_subgrid_level() From 26c1b7f3cb5e9b2dd2ecb90bf6fd7790b160c248 Mon Sep 17 00:00:00 2001 From: Martijn Visser Date: Fri, 26 Jan 2024 12:42:53 +0100 Subject: [PATCH 35/82] Use flow_rate rather than discharge in TabulatedRatingCurve (#992) A breaking change, but this is more consistent. Fixes #983. --- core/src/bmi.jl | 4 ++-- core/src/solve.jl | 2 +- core/src/utils.jl | 10 +++++----- core/src/validation.jl | 4 ++-- core/test/run_models_test.jl | 4 ++-- docs/core/equations.qmd | 4 ---- docs/core/usage.qmd | 6 +++--- docs/python/examples.ipynb | 8 ++++---- docs/schema/TabulatedRatingCurveStatic.schema.json | 4 ++-- docs/schema/TabulatedRatingCurveTime.schema.json | 4 ++-- python/ribasim/ribasim/models.py | 4 ++-- .../ribasim_testmodels/allocation.py | 6 +++--- python/ribasim_testmodels/ribasim_testmodels/basic.py | 6 +++--- .../ribasim_testmodels/discrete_control.py | 4 ++-- .../ribasim_testmodels/dutch_waterways.py | 4 ++-- .../ribasim_testmodels/ribasim_testmodels/equations.py | 4 ++-- .../ribasim_testmodels/ribasim_testmodels/invalid.py | 6 +++--- .../ribasim_testmodels/pid_control.py | 2 +- .../ribasim_testmodels/ribasim_testmodels/trivial.py | 2 +- ribasim_qgis/core/nodes.py | 4 ++-- 20 files changed, 44 insertions(+), 48 deletions(-) diff --git a/core/src/bmi.jl b/core/src/bmi.jl index 9b9a7993d..24c3b763a 100644 --- a/core/src/bmi.jl +++ b/core/src/bmi.jl @@ -607,9 +607,9 @@ function update_tabulated_rating_curve!(integrator)::Nothing # update the existing LinearInterpolation id = first(group).node_id level = [row.level for row in group] - discharge = [row.discharge for row in group] + flow_rate = [row.flow_rate for row in group] i = searchsortedfirst(node_id, NodeID(id)) - tables[i] = LinearInterpolation(discharge, level; extrapolate = true) + tables[i] = LinearInterpolation(flow_rate, level; extrapolate = true) end return nothing end diff --git a/core/src/solve.jl b/core/src/solve.jl index ab37fd191..f93a76ad5 100644 --- a/core/src/solve.jl +++ b/core/src/solve.jl @@ -121,7 +121,7 @@ end """ struct TabulatedRatingCurve{C} -Rating curve from level to discharge. The rating curve is a lookup table with linear +Rating curve from level to flow rate. The rating curve is a lookup table with linear interpolation in between. Relation can be updated in time, which is done by moving data from the `time` field into the `tables`, which is done in the `update_tabulated_rating_curve` callback. diff --git a/core/src/utils.jl b/core/src/utils.jl index 20ff9f75c..5ca7608b4 100644 --- a/core/src/utils.jl +++ b/core/src/utils.jl @@ -570,14 +570,14 @@ end function qh_interpolation( level::AbstractVector, - discharge::AbstractVector, + flow_rate::AbstractVector, )::Tuple{LinearInterpolation, Bool} - return LinearInterpolation(discharge, level; extrapolate = true), allunique(level) + return LinearInterpolation(flow_rate, level; extrapolate = true), allunique(level) end """ -From a table with columns node_id, discharge (Q) and level (h), -create a LinearInterpolation from level to discharge for a given node_id. +From a table with columns node_id, flow_rate (Q) and level (h), +create a LinearInterpolation from level to flow rate for a given node_id. """ function qh_interpolation( node_id::Int, @@ -585,7 +585,7 @@ function qh_interpolation( )::Tuple{LinearInterpolation, Bool} rowrange = findlastgroup(node_id, table.node_id) @assert !isempty(rowrange) "timeseries starts after model start time" - return qh_interpolation(table.level[rowrange], table.discharge[rowrange]) + return qh_interpolation(table.level[rowrange], table.flow_rate[rowrange]) end """ diff --git a/core/src/validation.jl b/core/src/validation.jl index 922b02fe2..8ff6e59cc 100644 --- a/core/src/validation.jl +++ b/core/src/validation.jl @@ -261,7 +261,7 @@ end node_id::Int active::Union{Missing, Bool} level::Float64 - discharge::Float64 + flow_rate::Float64 control_state::Union{Missing, String} end @@ -269,7 +269,7 @@ end node_id::Int time::DateTime level::Float64 - discharge::Float64 + flow_rate::Float64 end @version TerminalStaticV1 begin diff --git a/core/test/run_models_test.jl b/core/test/run_models_test.jl index 227ec010f..109c20dba 100644 --- a/core/test/run_models_test.jl +++ b/core/test/run_models_test.jl @@ -335,12 +335,12 @@ end See: https://en.wikipedia.org/wiki/Standard_step_method - * The left boundary has a fixed discharge `Q`. + * The left boundary has a fixed flow rate `Q`. * The right boundary has a fixed level `h_right`. * Channel profile is rectangular. # Arguments - - `Q`: discharge entering in the left boundary (m3/s) + - `Q`: flow rate entering in the left boundary (m3/s) - `w`: width (m) - `n`: Manning roughness - `h_right`: water level on the right boundary diff --git a/docs/core/equations.qmd b/docs/core/equations.qmd index 0ab8aeaa5..cc238d8a6 100644 --- a/docs/core/equations.qmd +++ b/docs/core/equations.qmd @@ -260,10 +260,6 @@ discharge. It can be understood as an empirical description of a basin's properties. This can include an outlet, but also the lumped hydraulic behavior of the upstream channels. - -The Tabulated Rating Curve should indicate at which volume no discharge occurs (the dead -storage volume). - :::{.callout-note} Currently, the discharge relies only on the basin's level; it could also use the volume of both connected basins to simulate backwater effects, submersion diff --git a/docs/core/usage.qmd b/docs/core/usage.qmd index e8e2789bd..6c7e3a529 100644 --- a/docs/core/usage.qmd +++ b/docs/core/usage.qmd @@ -393,9 +393,9 @@ node_id | Int | - | sorted control_state | String | - | (optional) sorted per node_id active | Bool | - | (optional, default true) level | Float64 | $m$ | sorted per control_state -discharge | Float64 | $m^3 s^{-1}$ | non-negative +flow_rate | Float64 | $m^3 s^{-1}$ | non-negative -node_id | discharge | level +node_id | flow_rate | level ------- |----------- |------- 2 | 0.0 | -0.105 2 | 0.0 | 0.095 @@ -416,7 +416,7 @@ column | type | unit | restriction node_id | Int | - | sorted time | DateTime | - | sorted per node_id level | Float64 | $m$ | - -discharge | Float64 | $m^3 s^{-1}$ | non-negative +flow_rate | Float64 | $m^3 s^{-1}$ | non-negative # Pump diff --git a/docs/python/examples.ipynb b/docs/python/examples.ipynb index 7b27083d2..13097eada 100644 --- a/docs/python/examples.ipynb +++ b/docs/python/examples.ipynb @@ -158,7 +158,7 @@ " data={\n", " \"node_id\": [4, 4],\n", " \"level\": [0.0, 1.0],\n", - " \"discharge\": [0.0, q1000],\n", + " \"flow_rate\": [0.0, q1000],\n", " }\n", " )\n", ")" @@ -867,7 +867,7 @@ "source": [ "rating_curve = ribasim.TabulatedRatingCurve(\n", " static=pd.DataFrame(\n", - " data={\"node_id\": 2 * [5], \"level\": [2.0, 15.0], \"discharge\": [0.0, 1e-3]}\n", + " data={\"node_id\": 2 * [5], \"level\": [2.0, 15.0], \"flow_rate\": [0.0, 1e-3]}\n", " )\n", ")" ] @@ -1633,7 +1633,7 @@ " data={\n", " \"node_id\": 7,\n", " \"level\": [0.0, 0.5, 1.0],\n", - " \"discharge\": [0.0, 0.0, 2.0],\n", + " \"flow_rate\": [0.0, 0.0, 2.0],\n", " }\n", " )\n", ")" @@ -1941,7 +1941,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.6" + "version": "3.11.7" } }, "nbformat": 4, diff --git a/docs/schema/TabulatedRatingCurveStatic.schema.json b/docs/schema/TabulatedRatingCurveStatic.schema.json index 0e21b91f0..319d37d8c 100644 --- a/docs/schema/TabulatedRatingCurveStatic.schema.json +++ b/docs/schema/TabulatedRatingCurveStatic.schema.json @@ -24,7 +24,7 @@ "format": "double", "type": "number" }, - "discharge": { + "flow_rate": { "format": "double", "type": "number" }, @@ -49,6 +49,6 @@ "required": [ "node_id", "level", - "discharge" + "flow_rate" ] } diff --git a/docs/schema/TabulatedRatingCurveTime.schema.json b/docs/schema/TabulatedRatingCurveTime.schema.json index 447df4100..52a07a442 100644 --- a/docs/schema/TabulatedRatingCurveTime.schema.json +++ b/docs/schema/TabulatedRatingCurveTime.schema.json @@ -17,7 +17,7 @@ "format": "double", "type": "number" }, - "discharge": { + "flow_rate": { "format": "double", "type": "number" }, @@ -32,6 +32,6 @@ "node_id", "time", "level", - "discharge" + "flow_rate" ] } diff --git a/python/ribasim/ribasim/models.py b/python/ribasim/ribasim/models.py index 38de5e958..87605768b 100644 --- a/python/ribasim/ribasim/models.py +++ b/python/ribasim/ribasim/models.py @@ -189,7 +189,7 @@ class TabulatedRatingCurveStatic(BaseModel): node_id: int active: bool | None = None level: float - discharge: float + flow_rate: float control_state: str | None = None remarks: str = Field("", description="a hack for pandera") @@ -198,7 +198,7 @@ class TabulatedRatingCurveTime(BaseModel): node_id: int time: datetime level: float - discharge: float + flow_rate: float remarks: str = Field("", description="a hack for pandera") diff --git a/python/ribasim_testmodels/ribasim_testmodels/allocation.py b/python/ribasim_testmodels/ribasim_testmodels/allocation.py index 4a218bd98..3be17b397 100644 --- a/python/ribasim_testmodels/ribasim_testmodels/allocation.py +++ b/python/ribasim_testmodels/ribasim_testmodels/allocation.py @@ -503,7 +503,7 @@ def looped_subnetwork_model(): data={ "node_id": [13, 13, 14, 14, 19, 19], "level": 3 * [0.0, 1.0], - "discharge": 3 * [0.0, 2.0], + "flow_rate": 3 * [0.0, 2.0], } ) ) @@ -784,7 +784,7 @@ def fractional_flow_subnetwork_model(): data={ "node_id": [3, 3], "level": [0.0, 1.0], - "discharge": [0.0, 1e-4], + "flow_rate": [0.0, 1e-4], } ) ) @@ -986,7 +986,7 @@ def allocation_example_model(): data={ "node_id": 7, "level": [0.0, 0.5, 1.0], - "discharge": [0.0, 0.0, 2.0], + "flow_rate": [0.0, 0.0, 2.0], } ) ) diff --git a/python/ribasim_testmodels/ribasim_testmodels/basic.py b/python/ribasim_testmodels/ribasim_testmodels/basic.py index 8d449d8c2..179d03a65 100644 --- a/python/ribasim_testmodels/ribasim_testmodels/basic.py +++ b/python/ribasim_testmodels/ribasim_testmodels/basic.py @@ -79,7 +79,7 @@ def basic_model() -> ribasim.Model: data={ "node_id": [4, 4], "level": [0.0, 1.0], - "discharge": [0.0, q1000], + "flow_rate": [0.0, q1000], } ) ) @@ -329,7 +329,7 @@ def tabulated_rating_curve_model() -> ribasim.Model: data={ "node_id": [2, 2], "level": [0.0, 1.0], - "discharge": [0.0, q1000], + "flow_rate": [0.0, q1000], } ), time=pd.DataFrame( @@ -345,7 +345,7 @@ def tabulated_rating_curve_model() -> ribasim.Model: pd.Timestamp("2020-03"), ], "level": [0.0, 1.0, 0.0, 1.1, 0.0, 1.2], - "discharge": [0.0, q1000, 0.0, q1000, 0.0, q1000], + "flow_rate": [0.0, q1000, 0.0, q1000, 0.0, q1000], } ), ) diff --git a/python/ribasim_testmodels/ribasim_testmodels/discrete_control.py b/python/ribasim_testmodels/ribasim_testmodels/discrete_control.py index e82b606a0..a1bb7f88c 100644 --- a/python/ribasim_testmodels/ribasim_testmodels/discrete_control.py +++ b/python/ribasim_testmodels/ribasim_testmodels/discrete_control.py @@ -524,7 +524,7 @@ def tabulated_rating_curve_control_model() -> ribasim.Model: data={ "node_id": [2, 2, 2, 2], "level": [0.0, 1.2, 0.0, 1.0], - "discharge": [0.0, q100, 0.0, q100], + "flow_rate": [0.0, q100, 0.0, q100], "control_state": ["low", "low", "high", "high"], } ), @@ -665,7 +665,7 @@ def level_setpoint_with_minmax_model(): # Setup the rating curve rating_curve = ribasim.TabulatedRatingCurve( static=pd.DataFrame( - data={"node_id": 2 * [5], "level": [2.0, 15.0], "discharge": [0.0, 1e-3]} + data={"node_id": 2 * [5], "level": [2.0, 15.0], "flow_rate": [0.0, 1e-3]} ) ) diff --git a/python/ribasim_testmodels/ribasim_testmodels/dutch_waterways.py b/python/ribasim_testmodels/ribasim_testmodels/dutch_waterways.py index e82e358f1..4920369f5 100644 --- a/python/ribasim_testmodels/ribasim_testmodels/dutch_waterways.py +++ b/python/ribasim_testmodels/ribasim_testmodels/dutch_waterways.py @@ -105,8 +105,8 @@ def dutch_waterways_model(): 7.46, 4.45, 4.46, - ], # The level and discharge for "pump_low", "pump_high" are irrelevant - "discharge": [0.0, 0.0] + ], # The level and flow rate for "pump_low", "pump_high" are irrelevant + "flow_rate": [0.0, 0.0] + 2 * [418, 420.15], # since the rating curve is not active here } ) diff --git a/python/ribasim_testmodels/ribasim_testmodels/equations.py b/python/ribasim_testmodels/ribasim_testmodels/equations.py index bbb678f11..87e9330a4 100644 --- a/python/ribasim_testmodels/ribasim_testmodels/equations.py +++ b/python/ribasim_testmodels/ribasim_testmodels/equations.py @@ -175,14 +175,14 @@ def rating_curve_model(): level_min = 1.0 node_id = np.full(n_datapoints, 2) level = np.linspace(0, 12, 100) - discharge = np.square(level - level_min) / (60 * 60 * 24) + flow_rate = np.square(level - level_min) / (60 * 60 * 24) rating_curve = ribasim.TabulatedRatingCurve( static=pd.DataFrame( data={ "node_id": node_id, "level": level, - "discharge": discharge, + "flow_rate": flow_rate, } ) ) diff --git a/python/ribasim_testmodels/ribasim_testmodels/invalid.py b/python/ribasim_testmodels/ribasim_testmodels/invalid.py index 7301f7f2a..c77bde12b 100644 --- a/python/ribasim_testmodels/ribasim_testmodels/invalid.py +++ b/python/ribasim_testmodels/ribasim_testmodels/invalid.py @@ -67,7 +67,7 @@ def invalid_qh_model(): rating_curve_static = pd.DataFrame( # Invalid: levels must not be repeated - data={"node_id": [1, 1], "level": [0.0, 0.0], "discharge": [1.0, 2.0]} + data={"node_id": [1, 1], "level": [0.0, 0.0], "flow_rate": [1.0, 2.0]} ) rating_curve_time = pd.DataFrame( data={ @@ -78,7 +78,7 @@ def invalid_qh_model(): ], # Invalid: levels must not be repeated "level": [0.0, 0.0], - "discharge": [1.0, 2.0], + "flow_rate": [1.0, 2.0], } ) @@ -195,7 +195,7 @@ def invalid_fractional_flow_model(): # Setup the tabulated rating curve: rating_curve = ribasim.TabulatedRatingCurve( static=pd.DataFrame( - data={"node_id": [7, 7], "level": [0.0, 1.0], "discharge": [0.0, 50.0]} + data={"node_id": [7, 7], "level": [0.0, 1.0], "flow_rate": [0.0, 50.0]} ) ) diff --git a/python/ribasim_testmodels/ribasim_testmodels/pid_control.py b/python/ribasim_testmodels/ribasim_testmodels/pid_control.py index 865067e42..095f506dd 100644 --- a/python/ribasim_testmodels/ribasim_testmodels/pid_control.py +++ b/python/ribasim_testmodels/ribasim_testmodels/pid_control.py @@ -256,7 +256,7 @@ def discrete_control_of_pid_control_model(): data={ "node_id": [4, 4], "level": [0.0, 1.0], - "discharge": [0.0, q1000], + "flow_rate": [0.0, q1000], } ) ) diff --git a/python/ribasim_testmodels/ribasim_testmodels/trivial.py b/python/ribasim_testmodels/ribasim_testmodels/trivial.py index 99b5067cf..4cca5a8a4 100644 --- a/python/ribasim_testmodels/ribasim_testmodels/trivial.py +++ b/python/ribasim_testmodels/ribasim_testmodels/trivial.py @@ -101,7 +101,7 @@ def trivial_model() -> ribasim.Model: data={ "node_id": [0, 0], "level": [0.0, 1.0], - "discharge": [0.0, q1000], + "flow_rate": [0.0, q1000], } ) ) diff --git a/ribasim_qgis/core/nodes.py b/ribasim_qgis/core/nodes.py index 20c63c2ed..84f240139 100644 --- a/ribasim_qgis/core/nodes.py +++ b/ribasim_qgis/core/nodes.py @@ -446,7 +446,7 @@ def attributes(cls) -> list[QgsField]: QgsField("node_id", QVariant.Int), QgsField("active", QVariant.Bool), QgsField("level", QVariant.Double), - QgsField("discharge", QVariant.Double), + QgsField("flow_rate", QVariant.Double), QgsField("control_state", QVariant.String), ] @@ -466,7 +466,7 @@ def attributes(cls) -> list[QgsField]: QgsField("time", QVariant.DateTime), QgsField("node_id", QVariant.Int), QgsField("level", QVariant.Double), - QgsField("discharge", QVariant.Double), + QgsField("flow_rate", QVariant.Double), ] From f4e90adbf8e345d72f1b9fef8cb4f567ee6a7f29 Mon Sep 17 00:00:00 2001 From: Huite Date: Fri, 26 Jan 2024 14:41:49 +0100 Subject: [PATCH 36/82] Add two_basin model to ribasim-testsmodels (#994) This model is only defined in the imod_coupler tests, which means it's not automatically updated when someone makes a breaking change. Then, the imod_coupler tests will fail. I'll update the fixture in imod_coupler after this is merged. --- .../ribasim_testmodels/__init__.py | 2 + .../ribasim_testmodels/two_basin.py | 126 ++++++++++++++++++ 2 files changed, 128 insertions(+) create mode 100644 python/ribasim_testmodels/ribasim_testmodels/two_basin.py diff --git a/python/ribasim_testmodels/ribasim_testmodels/__init__.py b/python/ribasim_testmodels/ribasim_testmodels/__init__.py index 0ddc0cfb1..f8c1f7d35 100644 --- a/python/ribasim_testmodels/ribasim_testmodels/__init__.py +++ b/python/ribasim_testmodels/ribasim_testmodels/__init__.py @@ -49,6 +49,7 @@ ) from ribasim_testmodels.time import flow_boundary_time_model from ribasim_testmodels.trivial import trivial_model +from ribasim_testmodels.two_basin import two_basin_model __all__ = [ "allocation_example_model", @@ -83,6 +84,7 @@ "minimal_subnetwork_model", "fractional_flow_subnetwork_model", "looped_subnetwork_model", + "two_basin_model", ] # provide a mapping from model name to its constructor, so we can iterate over all models diff --git a/python/ribasim_testmodels/ribasim_testmodels/two_basin.py b/python/ribasim_testmodels/ribasim_testmodels/two_basin.py new file mode 100644 index 000000000..5618ea7b1 --- /dev/null +++ b/python/ribasim_testmodels/ribasim_testmodels/two_basin.py @@ -0,0 +1,126 @@ +import geopandas as gpd +import numpy as np +import pandas as pd +import ribasim + + +def two_basin_model() -> ribasim.Model: + """ + Create a model of two basins. + + The basins are not connected; the model is mostly designed to test in + combination with a groundwater model. + + The left basin receives water. In case of a coupled run, the water + infiltrates in the left basin, and exfiltrates in the right basin. + The right basin fills up and discharges over the rating curve. + """ + flow_boundary = ribasim.FlowBoundary( + static=pd.DataFrame( + data={ + "node_id": [1], + "flow_rate": [1e-2], + } + ) + ) + + xy = np.array( + [ + (0, 0.0), # FlowBoundary + (250.0, 0.0), # Basin 1 + (750.0, 0.0), # Basin 2 + (1000.00, 0.0), # TabulatedRatingCurve + (1100.00, 0.0), # Terminal + ] + ) + # Rectangular profile + profile = pd.DataFrame( + data={ + "node_id": [2, 2, 3, 3], + "area": [400.0, 400.0, 400.0, 400.0], + "level": [0.0, 1.0, 0.0, 1.0], + } + ) + state = pd.DataFrame(data={"node_id": [2, 3], "level": [0.01, 0.01]}) + static = pd.DataFrame( + data={ + "node_id": [2, 3], + "drainage": [0.0, 0.0], + "potential_evaporation": [0.0, 0.0], + "infiltration": [0.0, 0.0], + "precipitation": [0.0, 0.0], + "urban_runoff": [0.0, 0.0], + } + ) + subgrid = pd.DataFrame( + data={ + "node_id": [2, 2, 3, 3], + "subgrid_id": [1, 1, 2, 2], + "basin_level": [0.0, 1.0, 0.0, 1.0], + "subgrid_level": [0.0, 1.0, 0.0, 1.0], + "meta_x": [250.0, 250.0, 750.0, 750.0], + "meta_y": [0.0, 0.0, 0.0, 0.0], + } + ) + basin = ribasim.Basin(profile=profile, state=state, static=static, subgrid=subgrid) + + rating_curve = ribasim.TabulatedRatingCurve( + static=pd.DataFrame( + data={ + "node_id": [4, 4], + "level": [0.0, 1.0], + "flow_rate": [0.0, 0.01], + } + ) + ) + + terminal = ribasim.Terminal( + static=pd.DataFrame( + data={ + "node_id": [5], + } + ) + ) + node_id, node_type = ribasim.Node.node_ids_and_types( + basin, + rating_curve, + flow_boundary, + terminal, + ) + node_xy = gpd.points_from_xy(x=xy[:, 0], y=xy[:, 1]) + + # Make sure the feature id starts at 1: explicitly give an index. + node = ribasim.Node( + df=gpd.GeoDataFrame( + data={"type": node_type}, + index=pd.Index(node_id, name="fid"), + geometry=node_xy, + crs="EPSG:28992", + ) + ) + + from_id = np.array([1, 3, 4], dtype=np.int64) + to_id = np.array([2, 4, 5], dtype=np.int64) + lines = node.geometry_from_connectivity([1, 3, 4], [2, 4, 5]) + edge = ribasim.Edge( + df=gpd.GeoDataFrame( + data={ + "from_node_id": from_id, + "to_node_id": to_id, + "edge_type": len(from_id) * ["flow"], + }, + geometry=lines, + crs="EPSG:28992", + ) + ) + + ribasim_model = ribasim.Model( + network=ribasim.Network(node=node, edge=edge), + basin=basin, + flow_boundary=flow_boundary, + tabulated_rating_curve=rating_curve, + terminal=terminal, + starttime="2020-01-01 00:00:00", + endtime="2030-01-01 00:00:00", + ) + return ribasim_model From 8a9a9285d17739c90d22b52fab266b64e8420d29 Mon Sep 17 00:00:00 2001 From: Martijn Visser Date: Fri, 26 Jan 2024 16:28:13 +0100 Subject: [PATCH 37/82] Always write fid index of Node and Edge tables (#995) We are using `GeoDataFrame.to_file` to write these tables to GeoPackage. By default GeoPandas only writes the index if it has a name. We don't want to rely on users naming indices, so this sets the name and ensure it is written. I ran into this since I noticed the `model.network.edge.df.index` (by default 0-based) did not correspond to the 1-based fid column that GeoPandas writes. https://geopandas.org/en/stable/docs/reference/api/geopandas.GeoDataFrame.to_file.html --- core/test/validation_test.jl | 6 +++--- python/ribasim/ribasim/input_base.py | 3 ++- python/ribasim/tests/test_model.py | 27 +++++++++++++++++++++++++-- 3 files changed, 30 insertions(+), 6 deletions(-) diff --git a/core/test/validation_test.jl b/core/test/validation_test.jl index 1d6dd4ce4..97b782b6d 100644 --- a/core/test/validation_test.jl +++ b/core/test/validation_test.jl @@ -250,7 +250,7 @@ end @test logger.logs[3].kwargs[:control_state] == "" @test logger.logs[4].level == Error @test logger.logs[4].message == "Cannot connect a basin to a fractional_flow." - @test logger.logs[4].kwargs[:edge_id] == 7 + @test logger.logs[4].kwargs[:edge_id] == 6 @test logger.logs[4].kwargs[:id_src] == NodeID(2) @test logger.logs[4].kwargs[:id_dst] == NodeID(8) end @@ -358,10 +358,10 @@ end @test length(logger.logs) == 2 @test logger.logs[1].level == Error @test logger.logs[1].message == - "Invalid edge type 'foo' for edge #1 from node #1 to node #2." + "Invalid edge type 'foo' for edge #0 from node #1 to node #2." @test logger.logs[2].level == Error @test logger.logs[2].message == - "Invalid edge type 'bar' for edge #2 from node #2 to node #3." + "Invalid edge type 'bar' for edge #1 from node #2 to node #3." end @testitem "Subgrid validation" begin diff --git a/python/ribasim/ribasim/input_base.py b/python/ribasim/ribasim/input_base.py index 17b066d01..8ba892e55 100644 --- a/python/ribasim/ribasim/input_base.py +++ b/python/ribasim/ribasim/input_base.py @@ -374,8 +374,9 @@ def _write_table(self, path: FilePath) -> None: gdf = gpd.GeoDataFrame(data=self.df) gdf = gdf.set_geometry("geometry") + gdf.index.name = "fid" - gdf.to_file(path, layer=self.tablename(), driver="GPKG") + gdf.to_file(path, layer=self.tablename(), driver="GPKG", index=True) def sort(self): self.df.sort_index(inplace=True) diff --git a/python/ribasim/tests/test_model.py b/python/ribasim/tests/test_model.py index 23da78e53..c59582d9e 100644 --- a/python/ribasim/tests/test_model.py +++ b/python/ribasim/tests/test_model.py @@ -136,10 +136,33 @@ def test_plot(discrete_control_of_pid_control): def test_write_adds_fid_in_tables(basic, tmp_path): model_orig = basic + # for node an explicit index was provided + nrow = len(model_orig.network.node.df) + assert model_orig.network.node.df.index.name == "fid" + assert model_orig.network.node.df.index.equals( + pd.RangeIndex(start=1, stop=nrow + 1) + ) + # for edge no index was provided, but it still needs to write it to file + nrow = len(model_orig.network.edge.df) + assert model_orig.network.edge.df.index.name is None + assert model_orig.network.edge.df.index.equals(pd.RangeIndex(start=0, stop=nrow)) + model_orig.write(tmp_path / "basic/ribasim.toml") with connect(tmp_path / "basic/database.gpkg") as connection: query = f"select * from {esc_id('Basin / profile')}" - df = pd.read_sql_query(query, connection, parse_dates=["time"]) + df = pd.read_sql_query(query, connection) assert "fid" in df.columns - fids = df.get("fid") + fids = df["fid"] assert fids.equals(pd.Series(range(1, len(fids) + 1))) + + query = "select fid from Node" + df = pd.read_sql_query(query, connection) + assert "fid" in df.columns + fids = df["fid"] + assert fids.equals(pd.Series(range(1, len(fids) + 1))) + + query = "select fid from Edge" + df = pd.read_sql_query(query, connection) + assert "fid" in df.columns + fids = df["fid"] + assert fids.equals(pd.Series(range(0, len(fids)))) From c7762fde2cabc0e6f57c070ff7625848ac59958a Mon Sep 17 00:00:00 2001 From: hofer_jn Date: Fri, 26 Jan 2024 16:30:42 +0100 Subject: [PATCH 38/82] TeamCity change in 'Ribasim / Windows' project: build features of 'Build ribasim_cli' build configuration were updated --- .../buildTypes/Ribasim_Windows_BuildRibasimCli.xml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/.teamcity/Ribasim_Windows/buildTypes/Ribasim_Windows_BuildRibasimCli.xml b/.teamcity/Ribasim_Windows/buildTypes/Ribasim_Windows_BuildRibasimCli.xml index 53a99c7db..42403143f 100644 --- a/.teamcity/Ribasim_Windows/buildTypes/Ribasim_Windows_BuildRibasimCli.xml +++ b/.teamcity/Ribasim_Windows/buildTypes/Ribasim_Windows_BuildRibasimCli.xml @@ -78,12 +78,6 @@ pixi run build-ribasim-cli]]> - - - - - - From 2acf180588d9a749216b698561862dfc07aa7cfd Mon Sep 17 00:00:00 2001 From: hofer_jn Date: Fri, 26 Jan 2024 16:54:40 +0100 Subject: [PATCH 39/82] TeamCity change in 'Ribasim' project: snapshot dependency was added in 'Make GitHub Release' build configuration --- .../buildTypes/Ribasim_Ribasim_MakeGitHubRelease.xml | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_MakeGitHubRelease.xml b/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_MakeGitHubRelease.xml index e9b85c898..9a781d1b3 100644 --- a/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_MakeGitHubRelease.xml +++ b/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_MakeGitHubRelease.xml @@ -105,37 +105,36 @@ fi]]> - + - + - + - + - + - From 52eb8598520ea1b7781cde889b5d6c06308882b4 Mon Sep 17 00:00:00 2001 From: hofer_jn Date: Fri, 26 Jan 2024 16:55:02 +0100 Subject: [PATCH 40/82] TeamCity change in 'Ribasim' project: snapshot dependency was added in 'Make GitHub Release' build configuration --- .../buildTypes/Ribasim_Ribasim_MakeGitHubRelease.xml | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_MakeGitHubRelease.xml b/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_MakeGitHubRelease.xml index 9a781d1b3..43fd70916 100644 --- a/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_MakeGitHubRelease.xml +++ b/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_MakeGitHubRelease.xml @@ -105,35 +105,34 @@ fi]]> - + - + - + - + - - + - - - - + + + + From f39accf9b466b0c62a00f11fd3818266a6136d18 Mon Sep 17 00:00:00 2001 From: hofer_jn Date: Fri, 26 Jan 2024 16:55:31 +0100 Subject: [PATCH 42/82] TeamCity change in 'Ribasim' project: snapshot dependency was added in 'Make GitHub Release' build configuration --- .../buildTypes/Ribasim_Ribasim_MakeGitHubRelease.xml | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_MakeGitHubRelease.xml b/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_MakeGitHubRelease.xml index 7e1c5e10c..4fd05955e 100644 --- a/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_MakeGitHubRelease.xml +++ b/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_MakeGitHubRelease.xml @@ -105,33 +105,32 @@ fi]]> - + - + - - + - + - + - + - - + - + - + - + - - - - + + + + From 194e2e8b9a63b34aa4c5b6a18112b753ae88de4e Mon Sep 17 00:00:00 2001 From: Hofer-Julian <30049909+Hofer-Julian@users.noreply.github.com> Date: Fri, 26 Jan 2024 20:31:01 +0100 Subject: [PATCH 45/82] Update version numbers (#996) In order to prepare for the release --- core/Project.toml | 2 +- python/ribasim/ribasim/__init__.py | 2 +- python/ribasim_api/ribasim_api/__init__.py | 2 +- ribasim_qgis/metadata.txt | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/core/Project.toml b/core/Project.toml index 7f7028348..2e22edab1 100644 --- a/core/Project.toml +++ b/core/Project.toml @@ -2,7 +2,7 @@ name = "Ribasim" uuid = "aac5e3d9-0b8f-4d4f-8241-b1a7a9632635" authors = ["Deltares and contributors "] manifest = "../Manifest.toml" -version = "0.6.0" +version = "0.7.0" [deps] Accessors = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" diff --git a/python/ribasim/ribasim/__init__.py b/python/ribasim/ribasim/__init__.py index c29a6902f..e7b2a7de9 100644 --- a/python/ribasim/ribasim/__init__.py +++ b/python/ribasim/ribasim/__init__.py @@ -1,4 +1,4 @@ -__version__ = "0.6.2" +__version__ = "0.7.0" from ribasim import models, utils diff --git a/python/ribasim_api/ribasim_api/__init__.py b/python/ribasim_api/ribasim_api/__init__.py index e7e218d63..d3d2ccdda 100644 --- a/python/ribasim_api/ribasim_api/__init__.py +++ b/python/ribasim_api/ribasim_api/__init__.py @@ -1,4 +1,4 @@ -__version__ = "0.5.0" +__version__ = "0.6.0" from ribasim_api.ribasim_api import RibasimApi diff --git a/ribasim_qgis/metadata.txt b/ribasim_qgis/metadata.txt index f7c46c4d1..61134b9ed 100644 --- a/ribasim_qgis/metadata.txt +++ b/ribasim_qgis/metadata.txt @@ -7,7 +7,7 @@ name=Ribasim-QGIS qgisMinimumVersion=3.0 description=QGIS plugin to setup Ribasim models -version=0.6 +version=0.7 author=Deltares and contributors email=ribasim.info@deltares.nl From 24e3a5b993834e3f9a90432d67846b463dad4465 Mon Sep 17 00:00:00 2001 From: Hofer-Julian <30049909+Hofer-Julian@users.noreply.github.com> Date: Mon, 29 Jan 2024 13:58:24 +0100 Subject: [PATCH 46/82] Allow compiled binaries to get version (#997) We started using the function that Julia provides, but it doesn't seem to work with compiled binaries Fixes #364 --- build/libribasim/src/libribasim.jl | 2 +- core/src/utils.jl | 13 +++++++++++++ python/ribasim_api/tests/test_bmi.py | 1 - 3 files changed, 14 insertions(+), 2 deletions(-) diff --git a/build/libribasim/src/libribasim.jl b/build/libribasim/src/libribasim.jl index ee216288f..448d68d02 100644 --- a/build/libribasim/src/libribasim.jl +++ b/build/libribasim/src/libribasim.jl @@ -175,7 +175,7 @@ end Base.@ccallable function get_version(version::Cstring)::Cint @try_c_uninitialized begin - ribasim_version = pkgversion(Ribasim) + ribasim_version = Ribasim.pkgversion(Ribasim) unsafe_write_to_cstring!(version, string(ribasim_version)) end end diff --git a/core/src/utils.jl b/core/src/utils.jl index 5ca7608b4..daeb1ca00 100644 --- a/core/src/utils.jl +++ b/core/src/utils.jl @@ -1,3 +1,16 @@ +"Get the package version of a given module" +function pkgversion(m::Module)::VersionNumber + version = Base.pkgversion(Ribasim) + !isnothing(version) && return version + + # Base.pkgversion doesn't work with compiled binaries + # If it returns `nothing`, we try a different way + rootmodule = Base.moduleroot(m) + pkg = Base.PkgId(rootmodule) + pkgorigin = get(Base.pkgorigins, pkg, nothing) + return pkgorigin.version +end + "Check that only supported edge types are declared." function valid_edge_types(db::DB)::Bool edge_rows = execute( diff --git a/python/ribasim_api/tests/test_bmi.py b/python/ribasim_api/tests/test_bmi.py index 01342a274..9d8664d6d 100644 --- a/python/ribasim_api/tests/test_bmi.py +++ b/python/ribasim_api/tests/test_bmi.py @@ -126,7 +126,6 @@ def test_get_component_name(libribasim): assert libribasim.get_component_name() == "Ribasim" -@pytest.mark.skip("https://github.com/Deltares/Ribasim/issues/364") def test_get_version(libribasim): toml_path = Path(__file__).parents[3] / "core" / "Project.toml" with open(toml_path, mode="rb") as fp: From 9a4473821ee62d0c9554c8bfd08db8a59916fb1e Mon Sep 17 00:00:00 2001 From: hofer_jn Date: Mon, 29 Jan 2024 14:19:07 +0100 Subject: [PATCH 47/82] TeamCity change in 'Ribasim' project: snapshot dependency was removed in 'Make GitHub Release' build configuration --- .../buildTypes/Ribasim_Ribasim_MakeGitHubRelease.xml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_MakeGitHubRelease.xml b/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_MakeGitHubRelease.xml index 3a5a3d029..d2699637a 100644 --- a/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_MakeGitHubRelease.xml +++ b/.teamcity/Ribasim/buildTypes/Ribasim_Ribasim_MakeGitHubRelease.xml @@ -98,12 +98,6 @@ fi]]> - - - - - - - -